Biomedical Informatics Research Network (BIRN)

BIRN Presentations

(Jump to BIRN Papers)

2013

DataSet Services in Globus Online. C. Kesselman and K. Chard, presented at the GlobusWorld Conference in Chicago, IL on April 17, 2013
Computing within the Cycle of Scientific Investigation. G. Burns, presented at the Beyond the PDF 2 Conference in Amsterdam, NL, March 20, 2013
How to Ride the Perfect Neuroimaging-Genetics-Computation Storm? Collision of Peta Bytes of Data, Thousands of Software Tools and Millions of Hardware Devices. I. Dinov, presented at the 2013 Pacific Rim Neuroimaging Conference in Oahu, Hawaii, March 5, 2013.
Enabling Collaboration Using the Biomedical Informatics Research Network (BIRN). B. Rosen, presented at the Quantitative Imaging Network Meeting in Bethesda, MD, March 4-5, 2013
Enabling Biomedical Collaboration with the Biomedical Informatics Research Network (BIRN). K. Helmer, poster presented at the Quantitative Imaging Network Meeting in Bethesda, MD, March 4-5, 2013

2012

BIRN Pathology Workbench and Virtual Slide Tools. K. Helmer, presented at the Pathology Informatics 2012 Conference in Chicago, IL, October 9-12, 2012
Connecting Brain Imaging Terms to Established Lexicons: a Precursor for Data Sharing and Querying. K.G. Helmer, S. Gosh, B.N. Nichols, D. Keator, T. Nichols, J. Turner, presented at the INCF Neuroinformatics 2012 Meeting in Munich, Germany, Sept 10-12, 2012
A System Architecture for Sharing De-Identified, Research-Ready Brain Scans and Health Information Across Clinical Imaging Centers. A.L. Chervenak, T.G.M. van Erp, C. Kesselman, M. D’Arcy, J. Sobell, D. Keator, L. Dahm, J. Murry, M. Law, A. Hasso, J. Ames, F. Macciardi and S.G. Potkin, presentation at the HealthGrid 2012 Conference in Amsterdam, NL, May 22, 2012
A Flexible, Open, Decentralized System for Digital Pathology Networks. R. Schuler, D.E. Smith, G. Kumaraguraparan, A. Chervenak, A.D. Lewis, D.M. Hyde, C. Kesselman, presenting at the HealthGrid 2012 Conference in Amsterdam, NL, May 22, 2012

2011

Visual Informatics and Genomics Using the Pipeline. F. Macciardi, F. Torri, I. Dinov and A. Toga, presenting at the 12th International Congress of Human Genetics (ICHG) and the 61st ASHG Annual Meeting in Montreal (Quebec), Canada, Oct 12, 2011.
Genomics Workflows progress (slides). F. Macciardi and I. Dinov, presenting at the 2011 BIRN AHM in Bethesda, MD, Sept 19, 2011.
Secure Data Management in BIRN. K. Helmer, presented at the INCF 2011 Neuroinformatics Meeting in Boston, MA, Sept 4-6, 2011
Visual Informatics and Computational Genomics Using the Graphical Pipeline Environment. I. Dinov presenting at the outGRID Workshop in Vilnius, Lithuania, April 11-14, 2011.
Pipeline Genomics and Informatics Webcast Video. I. Dinov presenting at the NIH Pipeline Demo online, Winter 2011

2010

Enabling Collaboration Using the Biomedical Informatics Research Network (BIRN). K.G. Helmer, presenting at the National Institute of Diabetes and Digestive and Kidney Diseases Informatics Working Group in Bethesda, MD, September 16, 2010.
Enabling Collaboration Using the Biomedical Informatics Research Network (BIRN). K.G. Helmer, presenting at the FaceBase All Hands Meeting in Pittsburgh, PA, June 4, 2010.
BIRN and the Grid: Informatics for Neuroimaging, Ian Foster, presenting at the Diffusion MRI of Traumatic Brain Injury Roadmap Workshop in Chicago, IL, June 2-3, 2010.
Multi-site Investigation of DTI Reproducibility. K. G. Helmer, M-C. Chou, A. Song, J. Turner, B. Gimi, and S. Mori, e-poster presentation at the Eighteenth Scientific Meeting of the International Society for Magnetic Resonance in Medicine, Stockholm, Sweden, May 1-7, 2010.

2009

BIRN Update – Carl Kesselman, Ph.D. National Center for Research Resources, September 15, 2009
Creating a Research Network using the Biomedical Informatics Research
Network (BIRN) – Karl Helmer, Ph.D. The Banbury Center, Cold Spring Harbor Laboratory, September 14, 2009

BIRN Papers

(Jump to BIRN Presentations)

2014

Keator DB, Fallon JH, Lakatos A, Fowlkes CC, Potkin SG, Ihler A; Alzheimer’s Disease Neuroimaging Initiative. Feed-forward hierarchical model of the ventral visual stream applied to functional brain image classification. Hum Brain Mapp. 2014 Jan. PUBMED PMID: 22847891

2013

Jiang Z, Dinov ID, Labus J, Shi Y, Zamanyan A, Gupta A, Ashe-McNalley C, Hong JY, Tillisch K, Toga AW, Mayer EA. Sex-related differences of cortical thickness in patients with chronic abdominal pain. PLoS One, 2013 Sep 5. PUBMED PMID: 24040118
Zhan J, Dinov ID, Li J, Zhang Z, Hobel S, Shi Y, Lin X, Zamanyan A, Feng L, Teng G, Fang F, Tang Y, Zang F, Toga AW, Liu S. Spatial-temporal atlas of human fetal brain development during the early second trimester. Neuroimage, 2013 Nov 15. PUBMED PMID: 23727529
Keator DB, Helmer K, Steffener J, Turner JA, Van Erp TG, Gadde S, Ashish N, Burns GA, Nichols BN. Towards structured sharing of raw and derived neuroimaging data across existing resources. Neuroimage, 2013 Nov. PUBMED PMID: 23727024
Burns, G. A. P. C. and Turner, J. A. Modeling Functional Magnetic Resonance Imaging (fMRI) Experimental Variables in the Ontology of Experimental Variables and Values (OoEVV). NeuroImage, 2013 Nov. PUBMED PMID: 23684873

2012

G. Konstantinidis and J.L. Ambite. (2012) Optimizing Query Rewriting for Multiple Queries. Proceedings of the 9th Workshop on Information Integration on the Web (IIWeb 2012). (Scottsdale, Arizona).
C. Ramakrishnan, A. Patnia, E. Hovy, and G.A.P.C. Burns. (2012) Layout-aware text extraction from full-text PDF of scientific articles. Source Code for Biology and Medicine 2012, 7:7. PMCID: PMC3441580
Tallis, M., Dave, D., and Burns, G.A. (2012). Preliminary meta-analyses of experimental design with examples from HIV vaccine protection studies. Discovery Informatics (Arlington VA).
Burns, G.A.P.C., and Turner, J.A. (2012). Bottom-up curation of terminology for experimental variables: the Ontology of Experimental Variables and Values (OoEVV). In Bio-Ontologies SIG, ISMB.
Burns, G.A.P.C., and Dave, D. (2012). A lightweight Ontology Design Pattern to curate and represent experimental variables from vaccine protection studies. In Vaccine and Drug Ontology in the Study of Mechanism and Effect, ICBO 2012.
Burns, G., Tallis, M., and Turner, J.A. (2012). Modeling Neuroanatomical Spatial Data Using the Ontology of Experimental Variables and Values (OoEVV). Proceedings of the INCF Meeting (Munich, Germany).
R. Schuler, D. E. Smith, G. Kumaraguruparan, A. Chervenak, A. D. Lewis, D. M. Hyde, and C. Kesselman. A Flexible, Open, Decentralized System for Digital Pathology Networks. In Healthgrid Applications and Technologies Meet Science Gateways for Life Sciences (Proceedings of the HealthGrid 2012 Conference), S. Gesing, et al., Ed.: IOS Press, 2012, p. 29. PUBMED PMID: 22941985
A. L. Chervenak, T. G. M. van Erp, C. Kesselman, M. D’Arcy, J. Sobell, D. Keator, L. Dahm, J. Murry, M. Law, and A. Hasso. A System Architecture for Sharing De-Identified, Research-Ready Brain Scans and Health Information Across Clinical Imaging Centers. In Healthgrid Applications and Technologies Meet Science Gateways for Life Sciences (Proceedings of the HealthGrid 2012 Conference), S. Gesing, et al., Ed.: IOS Press, 2012, p. 19. PUBMED PMID: 22941984
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. (2012) Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows, Genes, 3(3):545-575; doi:10.3390/genes3030545. PUBMED PMID: 23139896 PMCID: PMC3490498
Braden J, Foster I, Hauser T, Kettimuthu R, Martin S, Milroy D, Palen B, Tuecke S. (2012) Campus Bridging Made Easy via Globus Services. XSEDE12, July 16-20, 2012, Chicago, IL.
Allen B, Bresnahan J, Childers L, Foster I, Kandaswamy G, Kettimuthu R, Kordas J, Link M, Martin S, Pickett K, Tuecke S. (2012) Software as a Service for Data Scientists. Comm. ACM . 55, 81-88. doi :10.1145/ 2076450.2076468
Sansone S, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns GAPC, Chapman B, Clark T, Coleman L, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo C, Forster M, et al. (2012) Toward interoperable bioscience data. Nature Genetics 44, 121-126. doi:10.1038/ng.1054. PUBMED PMID: 22281772 PMCID: PMC3428019
INCF Neuroinformatics Congress 2012 Abstracts
- Connecting Brain Imaging Terms to Established Lexicons: a Precursor for Data Sharing and Querying
  Karl Helmer (Massachusetts General Hospital), Satrajit Ghosh (Massachusetts Institute of Technology), B. Nolan Nichols (University of Washington), David Keator (University of California, Irvine), Thomas Nichols (University of Warwick), Jessica Turner (The Mind Institute)
- XCEDE-DM: A neuroimaging extension to the W3C provenance data model
  Satrajit Ghosh (Massachusetts Institute of Technology), Nolan Nichols (Integrated Brain Imaging Center, University of Washington, Seattle, WA), Syam Gadde (Brain Imaging and Analysis Center, Duke University, Durham, NC), Jason Steffener (Columbia University, New York, NY), David Keator (Department of Psychiatry and Human Behavior, Department of Computer Science; University of California, Irvine)

2011

G. Konstantinidis and J.L. Ambite. (2011) Scalable Query Rewriting: A Graph-Based Approach. Proceedings of the ACM SIGMOD International Conference on Management of Data (SIGMOD 2011), (Athens, Greece).
Tallis M, Thompson R, Russ TA and Burns GAPC (2011) Knowledge synthesis with maps of neural connectivity. Front. Neuroinform. 5:24. doi: 10.3389/fninf.2011.00024. PUBMED PMID: 22053155
Thomas A Russ, Cartic Ramakrishnan, Eduard H Hovy, Mihail Bota and Gully APC Burns for the Biomedical Informatics Research Network. Knowledge Engineering Tools for Reasoning with Scientific Observations and Interpretations: a Neural Connectivity Use Case. BMC Bioinformatics 2011, 12:351doi:10.1186/1471-2105-12-351. 2011 Aug 22. PUBMED PMID: 21859449 PMCID: PMC3176268
Ivo D Dinov, Federica Torri, Fabio Macciardi, Petros Petrosyan, Zhizhong Liu, Alen Zamanyan, Paul Eggert, Jonathan Pierce, Alex Genco, James A Knowles, Andrew P Clark, John D Van Horn, Joseph Ames, Carl Kesselman and Arthur W Toga. Applications of the Pipeline Environment for Visual Informatics and Genomics Computations. BMC Bioinformatics, 12:304 (26 Jul 2011). PUBMED PMID: 21791102 PMCID: PMC3199760
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. for the Biomedical Informatics Research Network. (2011) Enabling collaborative research using the Biomedical Informatics Research Network (BIRN). J Am Med Inform Assoc. 2011 Apr 22; [Epub ahead of print] PUBMED PMID: 21515543.

2010

Dinov ID, Lozev K, Petrosyan P, Liu Z, Eggert P, Pierce, J, Zamanyan, A, Chakrapani, S, Van Horn, JD, Parker, DS, Magsipoc, R, Leung, K, Gutman, B, Woods, RP, Toga, AW. (2010) Neuroimaging Study Designs, Computational Analyses and Data Provenance Using the LONI Pipeline. PLoS ONE 5(9): e13070. doi:10.1371/journal.pone.0013070. PUBMED PMID: 20927408 PMCID: PMC2946935
Ashish N, Ambite JL, Muslea M and Turner JA (2010) Neuroscience data integration through mediation: an (F)BIRN case study. Front. Neuroinform. 4:118. doi: 10.3389/fninf.2010.00118. PUBMED PMID: 21228907 PMCID: PMC3017358
Kim, S., Smyth, P. and Stern, H. A Bayesian Mixture Approach to Modeling Spatial Activation Patterns in Multi-site fMRI Data. IEEE Transactions on Medical Imaging, 2010 Jun;29(6):1260-74. doi: 10.1109/TMI.2010.2044045. PUBMED PMID: 20304727

2009

Dinov I, Van Horn JD, Lozev KM, Magsipoc R, Petrosyan P, Liu Z, MacKenzie-Graham A, Eggert P, Parker DS and Toga AW (2009) Efficient, Distributed and Interactive Neuroimaging Data Analysis using the LONI Pipeline. Front. Neuroinform., 3(22):1-10. doi:10.3389/neuro.11.022.2009. PUBMED PMID: 19649168 PMCID: PMC2718780
David B. Keator, Dingying Wei, Syam Gadde, Jeremy Bockholt, Jeffrey S. Grethe, Daniel Marcus, Nicole Aucoin, Ibrahim B. Ozyurt. (2009). Derived Data Storage and Exchange Workflow for Large-Scale Neuroimaging Analyses on the BIRN Grid. Front. Neuroinformatics. 3: 30. doi: 10.3389/neuro.11.030.2009. PUBMED PMID: 19826494 PMCID: PMC2759340

2008

Keator, D.B.; Grethe, J.S.; Marcus, D.; Ozyurt, B.; Gadde, S.; Murphy, S.; Pieper, S.; Greve, D.;Notestine, R.; Bockholt, H.J.; Papadopoulos, P.; Function BIRN; Morphometry BIRN; BIRN Coordinating Center. (2008) A National Human Neuroimaging Collaboratory Enabled By The Biomedical Informatics Research Network (BIRN). IEEE Transactions on Information Technology in Biomedicine, Special Bio-Grid edition, 12 (2), 162-172. PUBMED PMID: 18348946 PMCID: PMC2763494
Leung, K, Parker, D, Cunha, A, Hojatkashani, C, Dinov, I, Toga, A (2008) IRMA: An Image Registration Meta-Algorithm. Lecture Notes in Computer Science, Springer Berlin/Heidelberg, vol 5069:612-617 DOI: 10.1007/978-3-540-69497-7_46

2004

Rex, DE, Shattuck, DW, Woods, RP, Narr, KL, Luders, E, Rehm, K, Stolzner, SE, Rottenberg, DA, Toga, AW (2004) A meta-algorithm for brain extraction in MRI. NeuroImage, Volume 23, Issue 2, October 2004, Pages 625-637, ISSN 1053-8119, DOI: 10.1016/j.neuroimage.2004.06.019. PUBMED PMID: 15488412

2003

Rex, DE, Ma, JQ, and Toga, AW. (2003) The LONI Pipeline Processing Environment. Neuroimage, 19(3): 1033-48. doi:10.1016/S1053-8119(03)00185-X. PUBMED PMID: 12880830

BIRN User Publications

You can find other BIRN-related publications here:

Function BIRN Publications

	Biomedical Informatics Research Network (BIRN) About About: Overview BIRN Video Introduction BIRN FAQs History Executive Committee Steering Committee Presentations/Papers Media Sponsors News Contact Us Capabilities Capabilities: Overview Demos and Downloads for Featured BIRN Capabilities Current Capabilities Working with BIRN Working with BIRN: Overview FAQ BIRN User Inquiry Working Groups Data Management Working Group Derived Data Working Group Genomics Working Group Information Integration Working Group Knowledge Engineering Working Group Operations Working Group Security Working Group Workflows Working Group Mailing Lists User Stories User Stories: Overview Multi-site fMRI Studies Resources Resources: Overview Tools Acquisition, Calibration and Quality Assurance Tools Analysis and Processing Tools Atlasing, Images and Visualization Tools Data Management and Collaboration Tools Ontologies, Standards and Terminologies Tools Security Tools Federated Informatics Research Environment (FIRE) Primer fMRI Scanner Calibration Methods and Recommendations fMRI Imaging Quality Assurance Methods Multi-site Cognitive Paradigms for fMRI studies Functional Imaging Calibration Paradigms All Tools Share Your Tools Software License Best Practices Supplemental Materials FBIRN Recommendations for Multi-Center fMRI Studies: Supplemental Material (JMRI cite) Supplement I: FBIRN Working Groups Supplement II: FBIRN Task presentation/psychometric collection Supplement III: FBIRN Scan parameters Supplement IV: FBIRN Quality Assurance Program Supplement V: FBIRN Informatics References Brain Morphometry Multi-site Studies Brain Morphometry Imaging Protocols Brain Morphometry MRI Phantom DTI Multisite Processing Functional MRI Multi-site Studies Data Alphabetical List of Data Collaborators Collaborators: Overview Radiation Oncology Pilot Project Taub Institute for Research at Columbia University Clinical Translational Science Institutes (CTSIs) Function BIRN Function BIRN Publications International Neuroinformatics Coordinating Facility (INCF) Cardiovascular Research Grid Presentations/Papers BIRN Presentations (Jump to BIRN Papers) 2013 DataSet Services in Globus Online. C. Kesselman and K. Chard, presented at the GlobusWorld Conference in Chicago, IL on April 17, 2013 Computing within the Cycle of Scientific Investigation. G. Burns, presented at the Beyond the PDF 2 Conference in Amsterdam, NL, March 20, 2013 How to Ride the Perfect Neuroimaging-Genetics-Computation Storm? Collision of Peta Bytes of Data, Thousands of Software Tools and Millions of Hardware Devices. I. Dinov, presented at the 2013 Pacific Rim Neuroimaging Conference in Oahu, Hawaii, March 5, 2013. Enabling Collaboration Using the Biomedical Informatics Research Network (BIRN). B. Rosen, presented at the Quantitative Imaging Network Meeting in Bethesda, MD, March 4-5, 2013 Enabling Biomedical Collaboration with the Biomedical Informatics Research Network (BIRN). K. Helmer, poster presented at the Quantitative Imaging Network Meeting in Bethesda, MD, March 4-5, 2013 2012 BIRN Pathology Workbench and Virtual Slide Tools. K. Helmer, presented at the Pathology Informatics 2012 Conference in Chicago, IL, October 9-12, 2012 Connecting Brain Imaging Terms to Established Lexicons: a Precursor for Data Sharing and Querying. K.G. Helmer, S. Gosh, B.N. Nichols, D. Keator, T. Nichols, J. Turner, presented at the INCF Neuroinformatics 2012 Meeting in Munich, Germany, Sept 10-12, 2012 A System Architecture for Sharing De-Identified, Research-Ready Brain Scans and Health Information Across Clinical Imaging Centers. A.L. Chervenak, T.G.M. van Erp, C. Kesselman, M. D’Arcy, J. Sobell, D. Keator, L. Dahm, J. Murry, M. Law, A. Hasso, J. Ames, F. Macciardi and S.G. Potkin, presentation at the HealthGrid 2012 Conference in Amsterdam, NL, May 22, 2012 A Flexible, Open, Decentralized System for Digital Pathology Networks. R. Schuler, D.E. Smith, G. Kumaraguraparan, A. Chervenak, A.D. Lewis, D.M. Hyde, C. Kesselman, presenting at the HealthGrid 2012 Conference in Amsterdam, NL, May 22, 2012 2011 Visual Informatics and Genomics Using the Pipeline. F. Macciardi, F. Torri, I. Dinov and A. Toga, presenting at the 12th International Congress of Human Genetics (ICHG) and the 61st ASHG Annual Meeting in Montreal (Quebec), Canada, Oct 12, 2011. Genomics Workflows progress (slides). F. Macciardi and I. Dinov, presenting at the 2011 BIRN AHM in Bethesda, MD, Sept 19, 2011. Secure Data Management in BIRN. K. Helmer, presented at the INCF 2011 Neuroinformatics Meeting in Boston, MA, Sept 4-6, 2011 Visual Informatics and Computational Genomics Using the Graphical Pipeline Environment. I. Dinov presenting at the outGRID Workshop in Vilnius, Lithuania, April 11-14, 2011. Pipeline Genomics and Informatics Webcast Video. I. Dinov presenting at the NIH Pipeline Demo online, Winter 2011 2010 Enabling Collaboration Using the Biomedical Informatics Research Network (BIRN). K.G. Helmer, presenting at the National Institute of Diabetes and Digestive and Kidney Diseases Informatics Working Group in Bethesda, MD, September 16, 2010. Enabling Collaboration Using the Biomedical Informatics Research Network (BIRN). K.G. Helmer, presenting at the FaceBase All Hands Meeting in Pittsburgh, PA, June 4, 2010. BIRN and the Grid: Informatics for Neuroimaging, Ian Foster, presenting at the Diffusion MRI of Traumatic Brain Injury Roadmap Workshop in Chicago, IL, June 2-3, 2010. Multi-site Investigation of DTI Reproducibility. K. G. Helmer, M-C. Chou, A. Song, J. Turner, B. Gimi, and S. Mori, e-poster presentation at the Eighteenth Scientific Meeting of the International Society for Magnetic Resonance in Medicine, Stockholm, Sweden, May 1-7, 2010. 2009 BIRN Update – Carl Kesselman, Ph.D. National Center for Research Resources, September 15, 2009 Creating a Research Network using the Biomedical Informatics Research Network (BIRN) – Karl Helmer, Ph.D. The Banbury Center, Cold Spring Harbor Laboratory, September 14, 2009 BIRN Papers (Jump to BIRN Presentations) 2014 Keator DB, Fallon JH, Lakatos A, Fowlkes CC, Potkin SG, Ihler A; Alzheimer’s Disease Neuroimaging Initiative. Feed-forward hierarchical model of the ventral visual stream applied to functional brain image classification. Hum Brain Mapp. 2014 Jan. PUBMED PMID: 22847891 2013 Jiang Z, Dinov ID, Labus J, Shi Y, Zamanyan A, Gupta A, Ashe-McNalley C, Hong JY, Tillisch K, Toga AW, Mayer EA. Sex-related differences of cortical thickness in patients with chronic abdominal pain. PLoS One, 2013 Sep 5. PUBMED PMID: 24040118 Zhan J, Dinov ID, Li J, Zhang Z, Hobel S, Shi Y, Lin X, Zamanyan A, Feng L, Teng G, Fang F, Tang Y, Zang F, Toga AW, Liu S. Spatial-temporal atlas of human fetal brain development during the early second trimester. Neuroimage, 2013 Nov 15. PUBMED PMID: 23727529 Keator DB, Helmer K, Steffener J, Turner JA, Van Erp TG, Gadde S, Ashish N, Burns GA, Nichols BN. Towards structured sharing of raw and derived neuroimaging data across existing resources. Neuroimage, 2013 Nov. PUBMED PMID: 23727024 Burns, G. A. P. C. and Turner, J. A. Modeling Functional Magnetic Resonance Imaging (fMRI) Experimental Variables in the Ontology of Experimental Variables and Values (OoEVV). NeuroImage, 2013 Nov. PUBMED PMID: 23684873 2012 G. Konstantinidis and J.L. Ambite. (2012) Optimizing Query Rewriting for Multiple Queries. Proceedings of the 9th Workshop on Information Integration on the Web (IIWeb 2012). (Scottsdale, Arizona). C. Ramakrishnan, A. Patnia, E. Hovy, and G.A.P.C. Burns. (2012) Layout-aware text extraction from full-text PDF of scientific articles. Source Code for Biology and Medicine 2012, 7:7. PMCID: PMC3441580 Tallis, M., Dave, D., and Burns, G.A. (2012). Preliminary meta-analyses of experimental design with examples from HIV vaccine protection studies. Discovery Informatics (Arlington VA). Burns, G.A.P.C., and Turner, J.A. (2012). Bottom-up curation of terminology for experimental variables: the Ontology of Experimental Variables and Values (OoEVV). In Bio-Ontologies SIG, ISMB. Burns, G.A.P.C., and Dave, D. (2012). A lightweight Ontology Design Pattern to curate and represent experimental variables from vaccine protection studies. In Vaccine and Drug Ontology in the Study of Mechanism and Effect, ICBO 2012. Burns, G., Tallis, M., and Turner, J.A. (2012). Modeling Neuroanatomical Spatial Data Using the Ontology of Experimental Variables and Values (OoEVV). Proceedings of the INCF Meeting (Munich, Germany). R. Schuler, D. E. Smith, G. Kumaraguruparan, A. Chervenak, A. D. Lewis, D. M. Hyde, and C. Kesselman. A Flexible, Open, Decentralized System for Digital Pathology Networks. In Healthgrid Applications and Technologies Meet Science Gateways for Life Sciences (Proceedings of the HealthGrid 2012 Conference), S. Gesing, et al., Ed.: IOS Press, 2012, p. 29. PUBMED PMID: 22941985 A. L. Chervenak, T. G. M. van Erp, C. Kesselman, M. D’Arcy, J. Sobell, D. Keator, L. Dahm, J. Murry, M. Law, and A. Hasso. A System Architecture for Sharing De-Identified, Research-Ready Brain Scans and Health Information Across Clinical Imaging Centers. In Healthgrid Applications and Technologies Meet Science Gateways for Life Sciences (Proceedings of the HealthGrid 2012 Conference), S. Gesing, et al., Ed.: IOS Press, 2012, p. 19. PUBMED PMID: 22941984 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. (2012) Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows, Genes, 3(3):545-575; doi:10.3390/genes3030545. PUBMED PMID: 23139896 PMCID: PMC3490498 Braden J, Foster I, Hauser T, Kettimuthu R, Martin S, Milroy D, Palen B, Tuecke S. (2012) Campus Bridging Made Easy via Globus Services. XSEDE12, July 16-20, 2012, Chicago, IL. Allen B, Bresnahan J, Childers L, Foster I, Kandaswamy G, Kettimuthu R, Kordas J, Link M, Martin S, Pickett K, Tuecke S. (2012) Software as a Service for Data Scientists. Comm. ACM . 55, 81-88. doi :10.1145/ 2076450.2076468 Sansone S, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns GAPC, Chapman B, Clark T, Coleman L, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo C, Forster M, et al. (2012) Toward interoperable bioscience data. Nature Genetics 44, 121-126. doi:10.1038/ng.1054. PUBMED PMID: 22281772 PMCID: PMC3428019 INCF Neuroinformatics Congress 2012 Abstracts Connecting Brain Imaging Terms to Established Lexicons: a Precursor for Data Sharing and Querying Karl Helmer (Massachusetts General Hospital), Satrajit Ghosh (Massachusetts Institute of Technology), B. Nolan Nichols (University of Washington), David Keator (University of California, Irvine), Thomas Nichols (University of Warwick), Jessica Turner (The Mind Institute) XCEDE-DM: A neuroimaging extension to the W3C provenance data model Satrajit Ghosh (Massachusetts Institute of Technology), Nolan Nichols (Integrated Brain Imaging Center, University of Washington, Seattle, WA), Syam Gadde (Brain Imaging and Analysis Center, Duke University, Durham, NC), Jason Steffener (Columbia University, New York, NY), David Keator (Department of Psychiatry and Human Behavior, Department of Computer Science; University of California, Irvine) 2011 G. Konstantinidis and J.L. Ambite. (2011) Scalable Query Rewriting: A Graph-Based Approach. Proceedings of the ACM SIGMOD International Conference on Management of Data (SIGMOD 2011), (Athens, Greece). Tallis M, Thompson R, Russ TA and Burns GAPC (2011) Knowledge synthesis with maps of neural connectivity. Front. Neuroinform. 5:24. doi: 10.3389/fninf.2011.00024. PUBMED PMID: 22053155 Thomas A Russ, Cartic Ramakrishnan, Eduard H Hovy, Mihail Bota and Gully APC Burns for the Biomedical Informatics Research Network. Knowledge Engineering Tools for Reasoning with Scientific Observations and Interpretations: a Neural Connectivity Use Case. BMC Bioinformatics 2011, 12:351doi:10.1186/1471-2105-12-351. 2011 Aug 22. PUBMED PMID: 21859449 PMCID: PMC3176268 Ivo D Dinov, Federica Torri, Fabio Macciardi, Petros Petrosyan, Zhizhong Liu, Alen Zamanyan, Paul Eggert, Jonathan Pierce, Alex Genco, James A Knowles, Andrew P Clark, John D Van Horn, Joseph Ames, Carl Kesselman and Arthur W Toga. Applications of the Pipeline Environment for Visual Informatics and Genomics Computations. BMC Bioinformatics, 12:304 (26 Jul 2011). PUBMED PMID: 21791102 PMCID: PMC3199760 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. for the Biomedical Informatics Research Network. (2011) Enabling collaborative research using the Biomedical Informatics Research Network (BIRN). J Am Med Inform Assoc. 2011 Apr 22; [Epub ahead of print] PUBMED PMID: 21515543. 2010 Dinov ID, Lozev K, Petrosyan P, Liu Z, Eggert P, Pierce, J, Zamanyan, A, Chakrapani, S, Van Horn, JD, Parker, DS, Magsipoc, R, Leung, K, Gutman, B, Woods, RP, Toga, AW. (2010) Neuroimaging Study Designs, Computational Analyses and Data Provenance Using the LONI Pipeline. PLoS ONE 5(9): e13070. doi:10.1371/journal.pone.0013070. PUBMED PMID: 20927408 PMCID: PMC2946935 Ashish N, Ambite JL, Muslea M and Turner JA (2010) Neuroscience data integration through mediation: an (F)BIRN case study. Front. Neuroinform. 4:118. doi: 10.3389/fninf.2010.00118. PUBMED PMID: 21228907 PMCID: PMC3017358 Kim, S., Smyth, P. and Stern, H. A Bayesian Mixture Approach to Modeling Spatial Activation Patterns in Multi-site fMRI Data. IEEE Transactions on Medical Imaging, 2010 Jun;29(6):1260-74. doi: 10.1109/TMI.2010.2044045. PUBMED PMID: 20304727 2009 Dinov I, Van Horn JD, Lozev KM, Magsipoc R, Petrosyan P, Liu Z, MacKenzie-Graham A, Eggert P, Parker DS and Toga AW (2009) Efficient, Distributed and Interactive Neuroimaging Data Analysis using the LONI Pipeline. Front. Neuroinform., 3(22):1-10. doi:10.3389/neuro.11.022.2009. PUBMED PMID: 19649168 PMCID: PMC2718780 David B. Keator, Dingying Wei, Syam Gadde, Jeremy Bockholt, Jeffrey S. Grethe, Daniel Marcus, Nicole Aucoin, Ibrahim B. Ozyurt. (2009). Derived Data Storage and Exchange Workflow for Large-Scale Neuroimaging Analyses on the BIRN Grid. Front. Neuroinformatics. 3: 30. doi: 10.3389/neuro.11.030.2009. PUBMED PMID: 19826494 PMCID: PMC2759340 2008 Keator, D.B.; Grethe, J.S.; Marcus, D.; Ozyurt, B.; Gadde, S.; Murphy, S.; Pieper, S.; Greve, D.;Notestine, R.; Bockholt, H.J.; Papadopoulos, P.; Function BIRN; Morphometry BIRN; BIRN Coordinating Center. (2008) A National Human Neuroimaging Collaboratory Enabled By The Biomedical Informatics Research Network (BIRN). IEEE Transactions on Information Technology in Biomedicine, Special Bio-Grid edition, 12 (2), 162-172. PUBMED PMID: 18348946 PMCID: PMC2763494 Leung, K, Parker, D, Cunha, A, Hojatkashani, C, Dinov, I, Toga, A (2008) IRMA: An Image Registration Meta-Algorithm. Lecture Notes in Computer Science, Springer Berlin/Heidelberg, vol 5069:612-617 DOI: 10.1007/978-3-540-69497-7_46 2004 Rex, DE, Shattuck, DW, Woods, RP, Narr, KL, Luders, E, Rehm, K, Stolzner, SE, Rottenberg, DA, Toga, AW (2004) A meta-algorithm for brain extraction in MRI. NeuroImage, Volume 23, Issue 2, October 2004, Pages 625-637, ISSN 1053-8119, DOI: 10.1016/j.neuroimage.2004.06.019. PUBMED PMID: 15488412 2003 Rex, DE, Ma, JQ, and Toga, AW. (2003) The LONI Pipeline Processing Environment. Neuroimage, 19(3): 1033-48. doi:10.1016/S1053-8119(03)00185-X. PUBMED PMID: 12880830 BIRN User Publications You can find other BIRN-related publications here: Function BIRN Publications About: Overview BIRN Video Introduction BIRN FAQs History Executive Committee Steering Committee Presentations/Papers Media Sponsors News Contact Us BIRN Collaboration wiki BIRN Documentation wiki Presentations/Papers Project Management ACCESS Account Management Copyright Privacy Sitemap Contact Us BIRN is supported by NIH grants 1U24-RR025736, U24-RR021992, U24-RR021760 and by the Collaborative Tools Support Network Award 1U24-RR026057-01.

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