Bertram Ludäscher

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2019

Computing environments for reproducibility: Capturing the “Whole Tale”

Brinckman, A., Chard, K., Gaffney, N., Hategan, M., Jones, M. B., Kowalik, K., Kulasekaran, S., Ludäscher, B., Mecum, B. D., Nabrzyski, J., Stodden, V., Taylor, I. J., Turk, M. J. & Turner, K., May 2019, In : Future Generation Computer Systems. 94, p. 854-867 14 p.

Research output: Contribution to journalArticle

PUG: a framework and practical implementation for why and why-not provenance

Lee, S., Ludäscher, B. & Glavic, B., Feb 1 2019, In : VLDB Journal. 28, 1, p. 47-71 25 p.

Research output: Contribution to journalArticle

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion

Franz, N. M., Musher, L. J., Brown, J. W., Yu, S. & Ludäscher, B., Feb 2019, In : PLoS computational biology. 15, 2, e1006493.

Research output: Contribution to journalArticle

Open Access
2017

Agreeing to disagree: Reconciling conflicting taxonomic views using a logic-based approach

Cheng, Y. Y., Franz, N., Schneider, J., Yu, S., Rodenhausen, T. & Ludäscher, B., Jan 1 2017, In : Proceedings of the Association for Information Science and Technology. 54, 1, p. 46-56 11 p.

Research output: Contribution to journalArticle

Insider Attack Identification and Prevention in Collection-Oriented Dataflow-Based Processes

Sarkar, A., Köhler, S., Ludäscher, B. & Bishop, M., Jun 2017, In : IEEE Systems Journal. 11, 2, p. 522-533 12 p.

Research output: Contribution to journalArticle

Logic-based schema alignment for natural history museum databases

Thomer, A., Cheng, Y. Y., Schneider, J., Twidale, M. & Ludascher, B., Jan 1 2017, In : Knowledge Organization. 44, 7, p. 545-558 14 p.

Research output: Contribution to journalArticle

Workflows and provenance: Toward information science solutions for the natural sciences

Gryk, M. R. & Ludäscher, B., Mar 1 2017, In : Library Trends. 65, 4, p. 555-562 8 p.

Research output: Contribution to journalArticle

2016

Decision-making system and operational risk framework for hierarchical production planning

Vargas, A., Day, S., Boza, A., Ortiz, A., Ludäscher, B., Sacala, I. S. & Moisescu, M. A., Jan 1 2016, In : Control Engineering and Applied Informatics. 18, 3, p. 72-81 10 p.

Research output: Contribution to journalArticle

Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building

Cui, H., Xu, D., Chong, S. S., Ramirez, M., Rodenhausen, T., Macklin, J. A., Ludäscher, B., Morris, R. A., Soto, E. M. & Koch, N. M., Nov 17 2016, In : BMC bioinformatics. 17, 1, 471.

Research output: Contribution to journalArticle

Names are not good enough: Reasoning over taxonomic change in the Andropogon complex

Franz, N. M., Chen, M., Kianmajd, P., Yu, S., Bowers, S., Weakley, A. S. & Ludäscher, B., Jan 1 2016, In : Semantic Web. 7, 6, p. 645-667 23 p.

Research output: Contribution to journalArticle

Two influential primate classifications logically aligned

Franz, N. M., Pier, N. M., Reeder, D. M., Chen, M., Yu, S., Kianmajd, P., Bowers, S. & Ludäscher, B., Jan 1 2016, In : Systematic biology. 65, 4, p. 561-582 22 p.

Research output: Contribution to journalArticle

Using a Computational Study of Hydrodynamics in the Wax Lake Delta to Examine Data Sharing Principles

Zhang, Q., Imker, H., Li, C., Ludäscher, B. & Senseney, M., 2016, In : International Journal of Digital Curation. 11, 2, p. 138-155

Research output: Contribution to journalArticle

2015

Reasoning over taxonomic change: Exploring alignments for the Perelleschus Use Case

Franz, N. M., Chen, M., Yu, S., Kianmajd, P., Bowers, S. & Ludäscher, B., Feb 20 2015, In : PloS one. 10, 2, e0118247.

Research output: Contribution to journalArticle

2013

AutoDrug: Fully automated macromolecular crystallography workflows for fragment-based drug discovery

Tsai, Y., McPhillips, S. E., González, A., McPhillips, T. M., Zinn, D., Cohen, A. E., Feese, M. D., Bushnell, D., Tiefenbrunn, T., Stout, C. D., Ludaescher, B., Hedman, B., Hodgson, K. O. & Soltis, S. M., May 1 2013, In : Acta Crystallographica Section D: Biological Crystallography. 69, 5, p. 796-803 8 p.

Research output: Contribution to journalArticle

Semantic annotation of mutable data

Morris, R. A., Dou, L., Hanken, J., Kelly, M., Lowery, D. B., Ludäscher, B., Macklin, J. A. & Morris, P. J., Nov 4 2013, In : PloS one. 8, 11, e76093.

Research output: Contribution to journalArticle

2012

Workflows for microarray data processing in the Kepler environment

Stropp, T., McPhillips, T., Ludäscher, B. & Bieda, M., May 17 2012, In : BMC bioinformatics. 13, 1, 102.

Research output: Contribution to journalArticle

2011

A data model for analyzing user collaborations in workflow-driven e-science

Altintas, I., Anand, M. K., Vuong, T. N., Bowers, S., Ludaescher, B. & Sloot, P. M. A., Sep 1 2011, In : International Journal of Computers and their Applications. 18, 3, p. 160-179 20 p.

Research output: Contribution to journalArticle

2010

Introducing W.A.T.E.R.S. A Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences

Hartman, A. L., Riddle, S., McPhillips, T., Ludäscher, B. & Eisen, J. A., Jun 12 2010, In : BMC bioinformatics. 11, 317.

Research output: Contribution to journalArticle

Parallelizing XML data-streaming workflows via MapReduce

Zinn, D., Bowers, S., Köhler, S. & Ludäscher, B., Jan 1 2010, In : Journal of Computer and System Sciences. 76, 6, p. 447-463 17 p.

Research output: Contribution to journalArticle

2009

Scientific workflow design for mere mortals

McPhillips, T., Bowers, S., Zinn, D. & Ludäscher, B., May 1 2009, In : Future Generation Computer Systems. 25, 5, p. 541-551 11 p.

Research output: Contribution to journalArticle

Sole-Search: An integrated analysis program for peak detection and functional annotation using ChIP-seq data

Blahnik, K. R., Dou, L., O'Geen, H., McPhillips, T., Xu, X., Cao, A. R., Iyengar, S., Nicolet, C. M., Ludäscher, B., Korf, I. & Farnham, P. J., Nov 10 2009, In : Nucleic acids research. 38, 3, p. e13.1-e13.17 gkp1012.

Research output: Contribution to journalArticle

2008

From computation models to models of provenance: The RWS approach

Ludäscher, B., Podhorszki, N., Altintas, I., Bowers, S. & McPhillips, T., Apr 10 2008, In : Concurrency Computation Practice and Experience. 20, 5, p. 507-518 12 p.

Research output: Contribution to journalArticle

Plasma edge kinetic-MHD modeling in tokamaks using Kepler workflow for code coupling, data management and visualization

Cummings, J., Pankin, A., Podhorszki, N., Park, G., Ku, S., Barreto, R., Klasky, S., Chang, C. S., Strauss, H., Sugiyama, L., Snyder, P., Pearlstein, D., Ludäscher, B., Bateman, G. & Kritz, A., Sep 2008, In : Communications in Computational Physics. 4, 3, p. 675-702 28 p.

Research output: Contribution to journalArticle

Provenance in collection-oriented scientific workflows

Bowers, S., McPhillips, T. M. & Ludäscher, B., Apr 10 2008, In : Concurrency Computation Practice and Experience. 20, 5, p. 519-529 11 p.

Research output: Contribution to journalArticle

Report on the principles of provenance workshop

Cheney, J., Buneman, P. & Ludäscher, B., Mar 1 2008, In : SIGMOD Record. 37, 1, p. 62-65 4 p.

Research output: Contribution to journalArticle

2007

A knowledge environment for the biodiversity and ecological sciences

Michener, W. K., Beach, J. H., Jones, M. B., Ludäscher, B., Pennington, D. D., Pereira, R. S., Rajasekar, A. & Schildhauer, M., Aug 1 2007, In : Journal of Intelligent Information Systems. 29, 1, p. 111-126 16 p.

Research output: Contribution to journalArticle

Interval-type and affine arithmetic-type techniques for handling uncertainty in expert systems

Ceberio, M., Kreinovich, V., Chopra, S., Longpré, L., Nguyen, H. T., Ludäscher, B. & Baral, C., Feb 15 2007, In : Journal of Computational and Applied Mathematics. 199, 2, p. 403-410 8 p.

Research output: Contribution to journalArticle

Reasoning about taxonomies in first-order logic

Thau, D. & Ludäscher, B., Oct 2007, In : Ecological Informatics. 2, 3 SPEC. ISS., p. 195-209 15 p.

Research output: Contribution to journalArticle

Rewriting queries using views with access patterns under integrity constraints

Deutsch, A., Ludäscher, B. & Nash, A., Mar 1 2007, In : Theoretical Computer Science. 371, 3, p. 200-226 27 p.

Research output: Contribution to journalArticle

SDM center technologies for accelerating scientific discoveries

Shoshani, A., Altintas, I., Choudhary, A., Critchlow, T., Kamath, C., Ludäscher, B., Nieplocha, J., Parker, S., Ross, R., Samatova, N. & Vouk, M., Jul 1 2007, In : Journal of Physics: Conference Series. 78, 1, 012068.

Research output: Contribution to journalArticle

Simulation of fusion plasmas: Current status and future direction

Batchelor, D. A., Beck, M., Becoulet, A., Budny, R. V., Chang, C. S., Diamond, P. H., Dong, J. Q., Fu, G. Y., Fukuyama, A., Hahm, T. S., Keyes, D. E., Kishimoto, Y., Klasky, S., Lao, L. L., Li, K., Lin, Z., Ludaescher, B., Manickam, J., Nakajima, N., Ozeki, T. & 9 others, Podhorszki, N., Tang, W. M., Vouk, M. A., Waltz, R. E., Wang, S. J., Wilson, H. R., Xu, X. Q., Yagi, M. & Zonca, F., Jun 1 2007, In : Plasma Science and Technology. 9, 3, p. 312-387 76 p.

Research output: Contribution to journalArticle

2006

Accelerating the scientific exploration process with scientific workflows

Altintas, I., Barney, O., Cheng, Z., Critchlow, T., Ludaescher, B., Parker, S., Shoshani, A. & Vouk, M., Oct 1 2006, In : Journal of Physics: Conference Series. 46, 1, p. 468-478 11 p., 065.

Research output: Contribution to journalArticle

Managing scientific data: From data integration to scientific workflows

Ludäscher, B., Lin, K., Bowers, S., Jaeger-Frank, E., Brodaric, B. & Baru, C., Jan 1 2006, In : Special Paper of the Geological Society of America. 397, p. 109-129 21 p.

Research output: Contribution to journalArticle

Report on the 2nd International Workshop on Data Integration in the Life Sciences

Gupta, A., Ludascher, B. & Raschid, L., Jan 1 2006, In : SIGMOD Record. 35, 2, p. 56-58 3 p.

Research output: Contribution to journalArticle

Report on the 2nd international workshop on Data Integration in the Life Sciences (DILS'05)

Gupta, A., Ludäscher, B. & Raschid, L., Jun 26 2006, In : SIGMOD Record. 35, 2, p. 57-59 3 p.

Research output: Contribution to journalArticle

Scientific workflow management and the Kepler system

Ludaescher, B., Altintas, I., Berkley, C., Higgins, D., Jaeger, E., Jones, M., Lee, E. A., Tao, J. & Zhao, Y., Aug 25 2006, In : Concurrency Computation Practice and Experience. 18, 10, p. 1039-1065 27 p.

Research output: Contribution to journalArticle

2005

Data management on the fusion computational pipeline

Klasky, S., Beck, M., Bhat, V., Feibush, E., Ludäscher, B., Parashar, M., Shoshani, A., Silver, D. & Vouk, M., Jan 1 2005, In : Journal of Physics: Conference Series. 16, 1, p. 510-520 11 p.

Research output: Contribution to journalArticle

2004
2003

The many faces of process interaction graphs: A data management perspective

Gupta, A. & Ludäscher, B., Jan 1 2003, In : OMICS A Journal of Integrative Biology. 7, 1, p. 105-107 3 p.

Research output: Contribution to journalArticle

Towards a formalization of disease-specific ontologies for neuroinformatics

Gupta, A., Ludäscher, B., Grethe, J. S. & Martone, M. E., Nov 2003, In : Neural Networks. 16, 9, p. 1277-1292 16 p.

Research output: Contribution to journalArticle

2002

A cell-centered database for electron tomographic data

Martone, M. E., Gupta, A., Wong, M., Qian, X., Sosinsky, G., Ludäscher, B. & Ellisman, M. H., Nov 20 2002, In : Journal of Structural Biology. 138, 1-2, p. 145-155 11 p.

Research output: Contribution to journalArticle

Report on the EDBT'02 panel on scientific data integration

Boucelma, O., Castano, S., Goble, C., Josifovski, V., Lacroix, Z. & Ludäscher, B., Dec 1 2002, In : SIGMOD Record. 31, 4, p. 107-112 6 p.

Research output: Contribution to journalArticle

Understanding the Global Semantics of Referential Actions using Logic Rules

May, W. & Ludäscher, B., Dec 1 2002, In : ACM Transactions on Database Systems. 27, 4, p. 343-397 55 p.

Research output: Contribution to journalArticle

2001

Preservation of digital data with self-validating, self-instantiating knowledge-based archives

Ludäscher, B., Marciano, R. & Moore, R., Sep 2001, In : SIGMOD Record (ACM Special Interest Group on Management of Data). 30, 3, p. 54-63 10 p.

Research output: Contribution to journalArticle

Towards a federated neuroscientific knowledge management system using brain atlases

Burns, G. A. P. C., Stephan, K., Ludäscher, B., Gupta, A. & Kötter, R., Jun 1 2001, In : Neurocomputing. 38-40, p. 1633-1641 9 p.

Research output: Contribution to journalArticle

2000

Collection-Based Persistent Digital Archives - Part 1

Moore, R., Baru, C., Rajasekar, A., Ludaescher, B., Marciano, R., Wan, M., Schroeder, W. & Gupta, A., Mar 2000, In : D-Lib Magazine. 6, 3

Research output: Contribution to journalArticle

Collection-based persistent digital archives - Part 2

Moore, R., Baru, C., Rajasekar, A., Ludaescher, B., Marciano, R., Wan, M., Schroeder, W. & Gupta, A., Apr 1 2000, In : D-Lib Magazine. 6, 4

Research output: Contribution to journalArticle

Games and total Datalog ¬ queries

Flum, J., Kubierschky, M. & Ludäscher, B., May 28 2000, In : Theoretical Computer Science. 239, 2, p. 257-276 20 p.

Research output: Contribution to journalArticle

Search Middleware and the Simple Digital Library Interoperability Protocol

Paepcke, A., Brandriff, R., Janee, G., Larson, R., Ludaescher, B., Melnik, S. & Raghavan, S., Mar 2000, In : D-Lib Magazine. 6, 3

Research output: Contribution to journalArticle