Publications

1. J. Baran, M. Gerner, M. Haeussler, G. Nenadic, C.M. Bergman, pubmed2ensembl: A Resource for Mining the Biological Literature on Genes, in PLoS ONE, volume 6, issue 9, e24716, doi:10.1371/journal.pone.0024716
2. J.M. Guberman, J. Ai, O. Arnaiz, J. Baran, A. Blake, R. Baldock, C. Chelala, D. Croft, A. Cros, R.J. Cutts, A. Di Genova, S. Forbes, T. Fujisawa, E. Gadaleta, D. M. Goodstein, G. Gundem, B. Haggarty, S. Haider, M. Hall, T. Harris, R. Haw, S. Hu, S. Hubbard, J. Hsu, V. Iyer, P. Jones, T. Katayama, R. Kinsella, L. Kong, D. Lawson, Y. Liang, N. Lopez-Bigas, J. Luo, M. Lush, J. Mason, F. Moreews, N. Ndegwa, D. Oakley, C. Perez-Llamas, M. Primig, E. Rivkin, S. Rosanoff, R. Shepherd, R. Simon, B. Skarnes, D. Smedley, L. Sperling, W. Spooner, P. Stevenson, K. Stone, J. Teague, J. Wang, J. Wang, B. Whitty, D. T. Wong, M. Wong-Erasmus, L. Yao, K. Youens-Clark, C. Yung, J. Zhang, A. Kasprzyk, BioMart Central Portal: an Open Database Network for the Biological Community, in Database, volume 2011, doi:10.1093/database/bar041
3. J. Zhang, S. Haider, J. Baran, A. Cros, J.M. Guberman, J. Hsu, Y. Liang, L. Yao, A. Kasprzyk, BioMart: a Data Federation Framework for Large Collaborative Projects, in Database, volume 2011, doi:10.1093/database/bar038
4. J. Zhang, J. Baran, A. Cros, J.M. Guberman, S. Haider, J. Hsu, Y. Liang, E. Rivkin, J. Wang, B. Whitty, M. Wong-Erasmus, L. Yao, A. Kasprzyk, International Cancer Genome Consortium Data Portal — a One-Stop Shop for Cancer Genomics Data, in Database, volume 2011, doi:10.1093/database/bar026
5. S. Pettifer, D. Thorne, P. McDermott, T. Attwood, J. Baran, J.C. Bryne, T. Hupponen, D. Mowbray, G. Vriend, An Active Registry for Bioinformatics Web Services, In Bioinformatics, volume 25, issue 16, pages 2090-2091, Oxford University Press, 2009, PMID 19460889, doi:10.1093/bioinformatics/btp329.
6. J. Baran, Handling Concatenation in Trace- and Model-Checking, PhD Thesis, 2009.
7. J. Baran and H. Barringer, Forays into Sequential Composition and Concatenation in EAGLE, In Proceedings of the 8th International Workshop on Runtime Verification, RV’08, volume 5289 of LNCS, pages 69-85, Springer, 2008, doi:10.1007/978-3-540-89247-2_5.
8. J. Baran and H. Barringer, A Grammatical Representation of Visibly Pushdown Languages, In Proceedings of the 14th Workshop on Logic, Language, Information and Computation, WoLLIC’07, volume 4576 of LNCS, pages 1-11, Springer, 2007, doi:10.1007/978-3-540-73445-1_1.