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Items: 1 to 50 of 77

1.

Virtual Excited State Reference for the Discovery of Electronic Materials Database: An Open-Access Resource for Ground and Excited State Properties of Organic Molecules.

Abreha BG, Agarwal S, Foster I, Blaiszik B, Lopez SA.

J Phys Chem Lett. 2019 Nov 7;10(21):6835-6841. doi: 10.1021/acs.jpclett.9b02577. Epub 2019 Oct 23.

PMID:
31642678
2.

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.

3.

BioWorkbench: a high-performance framework for managing and analyzing bioinformatics experiments.

Mondelli ML, Magalhães T, Loss G, Wilde M, Foster I, Mattoso M, Katz D, Barbosa H, de Vasconcelos ATR, Ocaña K, Gadelha LMR Jr.

PeerJ. 2018 Aug 29;6:e5551. doi: 10.7717/peerj.5551. eCollection 2018.

4.
5.

Toward a new generation of agricultural system data, models, and knowledge products: State of agricultural systems science.

Jones JW, Antle JM, Basso B, Boote KJ, Conant RT, Foster I, Godfray HCJ, Herrero M, Howitt RE, Janssen S, Keating BA, Munoz-Carpena R, Porter CH, Rosenzweig C, Wheeler TR.

Agric Syst. 2017 Jul;155:269-288. doi: 10.1016/j.agsy.2016.09.021.

6.

Brief history of agricultural systems modeling.

Jones JW, Antle JM, Basso B, Boote KJ, Conant RT, Foster I, Godfray HCJ, Herrero M, Howitt RE, Janssen S, Keating BA, Munoz-Carpena R, Porter CH, Rosenzweig C, Wheeler TR.

Agric Syst. 2017 Jul;155:240-254. doi: 10.1016/j.agsy.2016.05.014.

7.

Towards a new generation of agricultural system data, models and knowledge products: Information and communication technology.

Janssen SJC, Porter CH, Moore AD, Athanasiadis IN, Foster I, Jones JW, Antle JM.

Agric Syst. 2017 Jul;155:200-212. doi: 10.1016/j.agsy.2016.09.017.

8.

Sediment source fingerprinting for informing catchment management: Methodological approaches, problems and uncertainty.

Collins AL, Foster ID, Gellis AC, Porto P, Horowitz AJ.

J Environ Manage. 2017 Jun 1;194:1-3. doi: 10.1016/j.jenvman.2017.03.026. No abstract available.

PMID:
28390474
9.

Trace: a high-throughput tomographic reconstruction engine for large-scale datasets.

Bicer T, Gürsoy D, Andrade V, Kettimuthu R, Scullin W, Carlo F, Foster IT.

Adv Struct Chem Imaging. 2017;3(1):6. doi: 10.1186/s40679-017-0040-7. Epub 2017 Jan 28.

10.

Blending Education and Polymer Science: Semi Automated Creation of a Thermodynamic Property Database.

Tchoua RB, Qin J, Audus DJ, Chard K, Foster IT, de Pablo J.

J Chem Educ. 2016 Sep 13;93(9):1561-1568. Epub 2016 Aug 15.

11.

Sediment source fingerprinting as an aid to catchment management: A review of the current state of knowledge and a methodological decision-tree for end-users.

Collins AL, Pulley S, Foster ID, Gellis A, Porto P, Horowitz AJ.

J Environ Manage. 2017 Jun 1;194:86-108. doi: 10.1016/j.jenvman.2016.09.075. Epub 2016 Oct 12.

12.

Use of sediment source fingerprinting to assess the role of subsurface erosion in the supply of fine sediment in a degraded catchment in the Eastern Cape, South Africa.

Manjoro M, Rowntree K, Kakembo V, Foster I, Collins AL.

J Environ Manage. 2017 Jun 1;194:27-41. doi: 10.1016/j.jenvman.2016.07.019. Epub 2016 Aug 4.

PMID:
27499502
13.

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.

14.

Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions.

Li H, Achour I, Bastarache L, Berghout J, Gardeux V, Li J, Lee Y, Pesce L, Yang X, Ramos KS, Foster I, Denny JC, Moore JH, Lussier YA.

NPJ Genom Med. 2016;1. pii: 16006. Epub 2016 Apr 27.

15.

Optimization of tomographic reconstruction workflows on geographically distributed resources.

Bicer T, Gürsoy D, Kettimuthu R, De Carlo F, Foster IT.

J Synchrotron Radiat. 2016 Jul;23(Pt 4):997-1005. doi: 10.1107/S1600577516007980. Epub 2016 Jun 15.

16.

An Experimental Analysis of Children's Ability to Provide a False Report about a Crime.

Wyman J, Foster I, Talwar V.

J Vis Exp. 2016 May 3;(111). doi: 10.3791/53773.

17.

The impact of catchment source group classification on the accuracy of sediment fingerprinting outputs.

Pulley S, Foster I, Collins AL.

J Environ Manage. 2017 Jun 1;194:16-26. doi: 10.1016/j.jenvman.2016.04.048. Epub 2016 May 6.

PMID:
27160761
18.

Data publication with the structural biology data grid supports live analysis.

Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Fromme JC, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P.

Nat Commun. 2016 Mar 7;7:10882. doi: 10.1038/ncomms10882.

19.

A case study for cloud based high throughput analysis of NGS data using the globus genomics system.

Bhuvaneshwar K, Sulakhe D, Gauba R, Rodriguez A, Madduri R, Dave U, Lacinski L, Foster I, Gusev Y, Madhavan S.

Comput Struct Biotechnol J. 2014 Nov 7;13:64-74. doi: 10.1016/j.csbj.2014.11.001. eCollection 2015.

20.

A Hybrid Human-Computer Approach to the Extraction of Scientific Facts from the Literature.

Tchoua RB, Chard K, Audus D, Qin J, de Pablo J, Foster I.

Procedia Comput Sci. 2016;80:386-397. doi: 10.1016/j.procs.2016.05.338. Epub 2016 Jun 1.

21.

Globus Nexus: A Platform-as-a-Service Provider of Research Identity, Profile, and Group Management.

Chard K, Lidman M, McCollam B, Bryan J, Ananthakrishnan R, Tuecke S, Foster I.

Future Gener Comput Syst. 2016 Mar 1;56:571-583.

22.

Choosing experiments to accelerate collective discovery.

Rzhetsky A, Foster JG, Foster IT, Evans JA.

Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14569-74. doi: 10.1073/pnas.1509757112. Epub 2015 Nov 9.

23.

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.

24.

Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data.

Zhu Y, Xu Y, Helseth DL Jr, Gulukota K, Yang S, Pesce LL, Mitra R, Müller P, Sengupta S, Guo W, Silverstein JC, Foster I, Parsad N, White KP, Ji Y.

J Natl Cancer Inst. 2015 May 8;107(8). pii: djv129. doi: 10.1093/jnci/djv129. Print 2015 Aug.

25.

Globus Platform-as-a-Service for Collaborative Science Applications.

Ananthakrishnan R, Chard K, Foster I, Tuecke S.

Concurr Comput. 2015 Feb;27(2):290-305.

26.

NCI Workshop Report: Clinical and Computational Requirements for Correlating Imaging Phenotypes with Genomics Signatures.

Colen R, Foster I, Gatenby R, Giger ME, Gillies R, Gutman D, Heller M, Jain R, Madabhushi A, Madhavan S, Napel S, Rao A, Saltz J, Tatum J, Verhaak R, Whitman G.

Transl Oncol. 2014 Oct 24;7(5):556-69. doi: 10.1016/j.tranon.2014.07.007. eCollection 2014 Oct.

27.

Experiences Building Globus Genomics: A Next-Generation Sequencing Analysis Service using Galaxy, Globus, and Amazon Web Services.

Madduri RK, Sulakhe D, Lacinski L, Liu B, Rodriguez A, Chard K, Dave UJ, Foster IT.

Concurr Comput. 2014 Sep 10;26(13):2266-2279.

28.

'N-of-1-pathways' unveils personal deregulated mechanisms from a single pair of RNA-Seq samples: towards precision medicine.

Gardeux V, Achour I, Li J, Maienschein-Cline M, Li H, Pesce L, Parinandi G, Bahroos N, Winn R, Foster I, Garcia JG, Lussier YA.

J Am Med Inform Assoc. 2014 Nov-Dec;21(6):1015-25. doi: 10.1136/amiajnl-2013-002519. Epub 2014 Jun 12.

29.

Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes.

Trubetskoy V, Rodriguez A, Dave U, Campbell N, Crawford EL, Cook EH, Sutcliffe JS, Foster I, Madduri R, Cox NJ, Davis LK.

Bioinformatics. 2015 Jan 15;31(2):187-93. doi: 10.1093/bioinformatics/btu591. Epub 2014 Sep 29.

30.

Lynx web services for annotations and systems analysis of multi-gene disorders.

Sulakhe D, Taylor A, Balasubramanian S, Feng B, Xie B, Börnigen D, Dave UJ, Foster IT, Gilliam TC, Maltsev N.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W473-7. doi: 10.1093/nar/gku517. Epub 2014 Jun 19.

31.

Evaluating the utility of dynamical downscaling in agricultural impacts projections.

Glotter M, Elliott J, McInerney D, Best N, Foster I, Moyer EJ.

Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8776-81. doi: 10.1073/pnas.1314787111. Epub 2014 May 28.

32.

Supercomputing for the parallelization of whole genome analysis.

Puckelwartz MJ, Pesce LL, Nelakuditi V, Dellefave-Castillo L, Golbus JR, Day SM, Cappola TP, Dorn GW 2nd, Foster IT, McNally EM.

Bioinformatics. 2014 Jun 1;30(11):1508-13. doi: 10.1093/bioinformatics/btu071. Epub 2014 Feb 12.

33.

Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses.

Liu B, Madduri RK, Sotomayor B, Chard K, Lacinski L, Dave UJ, Li J, Liu C, Foster IT.

J Biomed Inform. 2014 Jun;49:119-33. doi: 10.1016/j.jbi.2014.01.005. Epub 2014 Jan 22.

34.

A spatial modeling framework to evaluate domestic biofuel-induced potential land use changes and emissions.

Elliott J, Sharma B, Best N, Glotter M, Dunn JB, Foster I, Miguez F, Mueller S, Wang M.

Environ Sci Technol. 2014 Feb 18;48(4):2488-96. doi: 10.1021/es404546r. Epub 2014 Feb 6.

PMID:
24456539
35.

Constraints and potentials of future irrigation water availability on agricultural production under climate change.

Elliott J, Deryng D, Müller C, Frieler K, Konzmann M, Gerten D, Glotter M, Flörke M, Wada Y, Best N, Eisner S, Fekete BM, Folberth C, Foster I, Gosling SN, Haddeland I, Khabarov N, Ludwig F, Masaki Y, Olin S, Rosenzweig C, Ruane AC, Satoh Y, Schmid E, Stacke T, Tang Q, Wisser D.

Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3239-44. doi: 10.1073/pnas.1222474110. Epub 2013 Dec 16.

36.

Attention-deficit/hyperactivity disorder subtype differentially predicts smoking expectancies in adolescents.

Foster I, Racicot S, McGrath JJ.

J Adolesc Health. 2012 Oct;51(4):393-9. doi: 10.1016/j.jadohealth.2012.01.014. Epub 2012 Mar 22.

37.

Gypsum-permineralized microfossils and their relevance to the search for life on Mars.

Schopf JW, Farmer JD, Foster IS, Kudryavtsev AB, Gallardo VA, Espinoza C.

Astrobiology. 2012 Jul;12(7):619-33. doi: 10.1089/ast.2012.0827. Epub 2012 Jul 13.

PMID:
22794252
38.

Towards an Oncology Database (ONCOD) Using a Warehousing Approach.

Wang X, Liu L, Fackenthal J, Chang P, Newstead G, Chmura S, Foster I, Olopade OI.

AMIA Jt Summits Transl Sci Proc. 2012;2012:105. Epub 2012 Mar 19.

39.

Research priorities. Shining light into black boxes.

Morin A, Urban J, Adams PD, Foster I, Sali A, Baker D, Sliz P.

Science. 2012 Apr 13;336(6078):159-60. doi: 10.1126/science.1218263. No abstract available.

40.

A Distributed Look-up Architecture for Text Mining Applications using MapReduce.

Balkir AS, Foster I, Rzhetsky A.

Proc Int Symp High Perform Distrib Comput. 2011 Nov;2011. doi: 10.1145/1996130.1996174.

41.

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.

42.

CaGrid Workflow Toolkit: a Taverna based workflow tool for cancer grid.

Tan W, Madduri R, Nenadic A, Soiland-Reyes S, Sulakhe D, Foster I, Goble CA.

BMC Bioinformatics. 2010 Nov 2;11:542. doi: 10.1186/1471-2105-11-542.

43.

A Comparison of Using Taverna and BPEL in Building Scientific Workflows: the case of caGrid.

Tan W, Missier P, Foster I, Madduri R, Goble C.

Concurr Comput. 2010 Jun 25;22(9):1098-1117.

44.

Soil erosion and risk-assessment for on- and off-farm impacts: a test case using the Midhurst area, West Sussex, UK.

Boardman J, Shepheard ML, Walker E, Foster ID.

J Environ Manage. 2009 Jun;90(8):2578-88. doi: 10.1016/j.jenvman.2009.01.018. Epub 2009 Feb 26.

PMID:
19249151
45.

e-Science, caGrid, and Translational Biomedical Research.

Saltz J, Kurc T, Hastings S, Langella S, Oster S, Ervin D, Sharma A, Pan T, Gurcan M, Permar J, Ferreira R, Payne P, Catalyurek U, Caserta E, Leone G, Ostrowski MC, Madduri R, Foster I, Madhavan S, Buetow KH, Shanbhag K, Siegel E.

Computer (Long Beach Calif). 2008 Nov;41(11):58-66.

46.

caGrid 1.0: a Grid enterprise architecture for cancer research.

Oster S, Langella S, Hastings S, Ervin D, Madduri R, Kurc T, Siebenlist F, Covitz P, Shanbhag K, Foster I, Saltz J.

AMIA Annu Symp Proc. 2007 Oct 11:573-7.

47.

A roadmap for caGrid, an enterprise Grid architecture for biomedical research.

Saltz J, Hastings S, Langella S, Oster S, Kurc T, Payne P, Ferreira R, Plale B, Goble C, Ervin D, Sharma A, Pan T, Permar J, Brezany P, Siebenlist F, Madduri R, Foster I, Shanbhag K, Mead C, Chue Hong N.

Stud Health Technol Inform. 2008;138:224-37.

48.

Interoperability of GADU in using heterogeneous grid resources for bioinformatics applications.

Sulakhe D, Rodriguez A, Wilde M, Foster I, Maltsev N.

IEEE Trans Inf Technol Biomed. 2008 Mar;12(2):241-6. doi: 10.1109/TITB.2007.897783.

PMID:
18348953
49.

caGrid 1.0: an enterprise Grid infrastructure for biomedical research.

Oster S, Langella S, Hastings S, Ervin D, Madduri R, Phillips J, Kurc T, Siebenlist F, Covitz P, Shanbhag K, Foster I, Saltz J.

J Am Med Inform Assoc. 2008 Mar-Apr;15(2):138-49. Epub 2007 Dec 20.

50.

Accelerating medical research using the swift workflow system.

Stef-Praun T, Clifford B, Foster I, Hasson U, Hategan M, Small SL, Wilde M, Zhao Y.

Stud Health Technol Inform. 2007;126:207-16.

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