GenaGrid

Publications

Selected publications in medical biology

1. Szalai C, Duba J, Prohászka Z, Kalina Á, Szabó T, Nagy B, Horváth L, Császár A. Involvement of polymorphisms in the chemokine system in the susceptibility for coronary artery disease (CAD). Coincidence of elevated Lp(a) and MCP-1 –2518 G/G genotype in CAD patients. Atherosclerosis 2001;158:233-239. IF 3,469

2. Szalai C, Kozma GT, Nagy A, Bojszkó Á, Krikovszky D, Szabó T, Falus A. Polymorphism in the gene regulatory region of MCP-1 is associated with asthma susceptibility and severity. J Allergy Clin Immunol 2001 Sep;108(3):375-381. IF.: 5,506

3. Szalai C, Füst G, Duba J, Kramer J, Romics L, Prohászka Z, Császár A. Association of polymorphisms and allelic combinations in the tumor necrosis factor--complement MHC region with coronary artery disease. J Med Genet 2002; 39:46-51. IF.: 5,098

4. Igaz P, Fitzimons CP, Szalai C, Falus A. Histamine genomics in silico: polymorphisms of the human genes involved in the synthesis, action and degradation of histamine. Am J Pharmacogenomics 2002;2(1):67-72.

5. Kozma GT, Losonczy G, Keszei M, Komlósi Z, Buzás E, Pállinger É, Appel J, Szabó T, Magyar P, Falus A, Szalai C. Histamine deficiency in gene-targeted mice strongly reduces antigen-induced airway hyperresponsiveness, eosinophilia and allergen specific IgE. Int Immunol. 2003 Aug;15(8):963-73. IF.: 3,611

6. Vatay A, Bene L, Kovacs A, Prohaszka Z, Szalai C, Romics L, Fekete B, Karadi I, Fust G. Relationship between the tumor necrosis factor alpha polymorphism and the serum C-reactive protein levels in inflammatory bowel disease. Immunogenetics. 2003 Jul;55(4):247-52.IF.: 2,268

7. Yang Y, Chung EK, Zhou B, Blanchong CA, Yu CY, Fust G, Kovacs M, Vatay A, Szalai C, Karadi I, Varga L Diversity in intrinsic strengths of the human complement system: serum C4 protein concentrations correlate with C4 gene size and polygenic variations, hemolytic activities, and body mass index. J Immunol. 2003 Sep 1;171(5):2734-45.IF.: 7,065

8. Szalai C, Keszei M, Duba J, Prohaszka Z, Kozma GT, Csaszar A, Balogh S, Almassy Z, Fust G, Czinner A. Polymorphism in the promoter region of the apolipoprotein A5 gene is associated with an increased susceptibility for coronary artery disease. Atherosclerosis 2004;173 (1): 109-114. IF.: 3,333

9. Fust G, Arason GJ, Kramer J, Szalai C, Duba J, Yang Y, Chung EK, Zhou B, Blanchong CA, Lokki ML, Bodvarsson S, Prohaszka Z, Karadi I, Vatay A, Kovacs M, Romics L, Thorgeirsson G, Yu CY.. Genetic Basis of Tobacco Smoking: Strong Association of a Specific Major Histocompatibility Complex (MHC) Haplotype on Chromosome 6 with Smoking Behavior. Int Immunol. 2004 Oct;16(10):1507-14.. IF.:3,611

10. Gergely Tölgyesi, Márton Keszei, Ildikó Ungvári, Adrienne Nagy, András Falus, Csaba Szalai. Involvement of TNF -308A promoter polymorphism in the development of asthma in children infected with Chlamydophila pneumoniae. Pediatr Res. 2006 Nov; 60(5):543-8. IF.: 2,875

11. Ildikó Ungvári, Gergely Tölgyesi, Ágnes F. Semsei, Adrienne Nagy, Károly Radosits, Márton Keszei, Gergely T Kozma, András Falus, Csaba Szalai. CCR5Δ32 mutation, Mycoplasma pneumoniae infection and asthma. J Allergy Clin Immunol. 2007 Jun;119(6):1545-7. Epub 2007 Apr 18, IF.: 8,829

12. Erdelyi DJ, Kamory E, Zalka A, Semsei AF, Csokay B, Andrikovics H, Tordai A, Borgulya G, Magyarosy E, Galantai I, Fekete G, Falus A, Szalai C, Kovacs GT. The role of ABC-transporter gene polymorphisms in chemotherapy induced immunosuppression, a retrospective study in childhood acute lymphoblastic leukaemia. Cell Immunol. 2006 Dec;244(2):121-4. Epub 2007 Apr 16. IF.: 1,709

13. Kiszel P, Kovacs M, Szalai C, Yang Y, Pozsonyi E, Blasko B, Laki J, Prohaszka Z, Fazakas A, Panczel P, Hosszufalusi N, Rajczy K, Wu YL, Chung EK, Zhou B, Blanchong CA, Vatay A, Yu CY, Fust G. Frequency of carriers of 8.1 ancestral haplotype and its fragments in two Caucasian populations. Immunol Invest. 2007;36(3):307-19. IF.: 1,276

14. Erdélyi DJ, Kámory E, Csókay B, Andrikovics H, Tordai A, Kiss C, Félné-Semsei Á, Janszky I, Zalka A, Fekete G, Falus A, Kovács GT, Szalai C. Synergistic interaction of ABCB1 and ABCG2 polymorphisms predicts the prevalence of toxic encephalopathy during anticancer chemotherapy. Pharmacogenomics J. 2008 8: 321-327. IF.: 5,435

15. Semsei ÁF, Erdélyi DJ, Ungvári I, Kámory E, Csókay B, Andrikovics H, Tordai A, Cságoly E, Falus A, Kovács GT, Szalai C. Association of some rare haplotypes and genotype combinations in the MDR1 gene with childhood acute lymphoblastic leukaemia. Leukemia Res. 2008 Aug;32(8):1214-20.IF.: 2,483

16. Csaba Szalai, Ildikó Ungvári, Liza Pelyhe, Gergely Tölgyesi, András Falus. Asthma from a pharmacogenomic point of view. Brit J Pharmacol. 2008 Apr;153(8):1602-14. IF.: 4,902

17. Tölgyesi G, Molnár V, Semsei ÁF, Kiszel P, Ungvári I, Pócza P, Wiener Z, Komlósi ZI, Kunos L, Gálffy G, Losonczy G, Seres I, Falus A, Szalai C. Gene expression profiling of experimental asthma reveals a possible role of paraoxonase-1 in the disease. Int Immunol. 2009 Aug;21(8):967-75. IF.: 3,290

18. Semsei AF, Antal P, Szalai C. Strengths and weaknesses of gene association studies in childhood acute lymphoblastic leukemia. Leuk Res. 2010: 34:269-271. IF.: 2,483

19. Szabó PM, V Tamási, V Molnár, M Andrásfalvy, Z Tömböl, R Farkas, K Kövesdi, A Patócs, M Tóth, C Szalai, A Falus, K Rácz and P Igaz Meta-analysis of adrenocortical tumour genomics data: novel pathogenic pathways revealed. Oncogene advance online publication, March 22, 2010; doi:10.1038/onc.2010.80; IF.: 7.216

20. Sherborne AL, Hosking FJ, Prasad BR, Kumar R, Rolf Koehler R, Vijayakrishnan J… Szalai C, et al. Variation in CDKN2A at 9p21.3 influences childhood acute lymphoblastic leukemia risk. Nat Genet. Epub 2010 May 9; DOI 10.1038/ng.585. IF.: 30.259

21. Triglyceride Coronary Disease Genetics Consortium (Szalai C et al) and Emerging Risk Factors Collaboration. Triglyceride-mediated pathways and coronary disease: collaborative analysis of 101 studies. Lancet. 2010 May 8;375(9726):1634-9. IF.: 28.409

Selected publications in bioinformatics

Chapters

P. Antal, A. Millinghoffer, G. Hullám, G. Hajós, Cs. Szalai, A. Falus: A bioinformatic platform for a Bayesian, multiphased, multilevel analysis in immunogenomics, in Bioinformatics for Immunomics, Ed.: M.N.Davies, S.Ranganathan, D.R.Flower, Springer, 2009

Journal papers

1.P. Antal, G. Fannes, D. Timmerman, Y. Moreau, B. De Moor: Bayesian Applications of Belief Networks and Multilayer Perceptrons for Ovarian Tumor Classification with Rejection, Artificial Intelligence in Medicine, vol. 29, pp 39-60, 2003, IF: 1.222

2. P. Antal, G. Fannes, Y. Moreau, D. Timmerman, B. De Moor: Using Literature and Data to Learn Bayesian Networks as Clinical Models of Ovarian Tumors, Artificial Intelligence in Medicine, 2004, vol 30, pp 257-281, IF: 1.124

3. Y. Moreau, P. Antal, G. Fannes, B. De Moor: Probabilistic graphical models for computational biomedicine, Methods of Information in Medicine, 2003; 42(2) pp. 161-8., IF: 1.092

4. P. Antal, G. Fannes, Y. Moreau, B. De Moor, J Vandewalle, D. Timmerman: Extended Bayesian regression models: a symbiotic application of Belief Networks and Multilayer Perceptrons for the Classification of Ovarian Tumors, in: AIME 2001. Lecture Notes in Artificial Intelligence 2001, Springer-Verlag, Berlin, 2001, pp 177-187,

5. P. Antal, A. Millinghoffer, G. Hullám: Statisztikai adat- és szövegelemzés Bayes-hálókkal: a valószínűségektől a függetlenségi és oksági viszonyokig, Híradástechnika, 2005, vol. 60, pp 40-49

6. P. Antal, A. Millinghoffer: Learning Causal Bayesian Networks from Literature Data, Periodica Polytechnica, 2006, vol. 40, no. 3-4, pp 201-221

7. T. G Szabó, R. Palotai, P. Antal, I. Tokatly, L. Tóthfalusi, O. Lund, Gy. Nagy, A. Falus, E. I. Buzás: Critical role of glycosylation in determining the length and structure of T cell epitopes- As suggested by a combined in silico systems biology approach, Immunome Research, (accepted), IF: 5.33

8. Semsei A.F, Antal P, Szalai Cs.: Strengths and weaknesses of gene association studies in childhood acute lymphoblastic leukemia, Leuk Res., 2009, in press, doi:10.1016/j.leukres.2009.07.036, IF: 2.39

9. Sanjeev Srivastava, Péter Antal, Mercédesz Mazán, Mária Pásztói, Ilona Újfalussy, Bernadett Rojkovich, Judit Kelemen, Ildikó Ungvári, Csaba Szalai, Tamás Gáti, Gábor Hullám, György Nagy, András Falus, Edit I Buzás: Combined analysis of two single nucleotide polymorphisms of the glucuronidase gene shows strong association with rheumatoid arthritis, The Journal of Rheumatology (submitted)

10. S. Srivastava, P. Antal, J. Gál, G. Hullám, A.F. Semsei, G. Nagy, A. Falus, E. I. Buzás: Lack of evidence for association of two functional SNPs of CHI3L1 gene(HC-gp39) with rheumatoid arthritis, Rheumatology International (Clinical and Experimental Investigations), 2010

11. G. Hullám, P. Antal, Cs. Szalai, A. Falus: Evaluation of a Bayesian model-based approach in GA studies, JMLR Workshop and Conference Proceedings, 2010

Conference papers

1.P. Antal: Applicability of Prior Domain Knowledge Formalised as Bayesian Network in the Process of Construction of a Classifier, IEEE IECON’98, 1998, Aachen, pp. 2527-2531

2. P. Antal, H. Verrelst, D. Timmerman, S. Van Huffel, B. De Moor, I. Vergote, Y. Moreau: Bayesian networks in ovarian cancer diagnosis: potentials and limitations, 13th IEEE Symposium on Computer-Based Medical Systems, June 23-24, 2000, Texas Medical Center, Houston, Texas, pp. 103-108

3. P. Antal, H. Verrelst, D. Timmerman, S. Van Huffel, B. De Moor, I. Vergote: How might we combine the information we know about a mass better? The use of mathematical models to handle medical data, 1st Montecarlo Conference on updates in Gynaecology, March 8-11, 2000, Monaco

4. P. Antal, G. Fannes, H. Verrelst, B. De Moor, J Vandewalle: Incorporation of prior knowledge in black-box models: Comparison of Transformation Methods from Bayesian Network to Multilayer Perceptrons, in Working notes of the Fusion of Domain Knowledge with Data for Decision Support workshop, The Sixteenth Conference on Uncertainty in Artificial Intelligence (UAI-2000), June 30, 2000, Stanford University, pp. 11-16

5. P. Antal, G. Fannes, S. Van Huffel, B. De Moor, J Vandewalle: Bayesian predictive models for Ovarian Cancer Classification: evaluation of Logistic Regression, Multi Layer Perceptron and Belief Network models in the Bayesian Context, Proc. Of the 10th Belgian-Dutch Conf. On Machine Learning, BENELEARN2000, December 13, 2000, Tilburg University, pp. 125-132

6. P. Antal, G. Fannes, De Smet F., B. De Moor: Ovarian cancer classification with rejection by Bayesian Belief Networks, in Working Notes of the Bayesian Models in Medicine workshop, the European Conference on Artificial Intelligence in Medicine (AIME'01), 8th European Conference on Artificial Intelligence in Medicine, AIME'01, July 1-4, 2001, Cascais, Portugal, pp 23-27

7. P. Antal, T. Meszaros, B. De Moor, T. Dobrowiecki: Annotated Bayesian networks: a tool to integrate textual and probabilistic medical knowledge, Fourteenth IEEE Symposium on Computer-Based Medical Systems (CBMS 2001), July 26-27, Bethesda, MD, pp. 177-182

8. P. Antal, T. Meszaros, D. Timmerman, B. De Moor, T. Dobrowiecki: Domain knowledge based information retrieval langugae: an application of annotated Bayesian networks, Fifteenth IEEE Symposium on Computer-Based Medical Systems (CBMS 2002), June 3-7, Maribor, Slovenia, pp 213-218

9. S. Aerts, P. Antal, B. De Moor, Y. Moreau: Web-based data collection for ovarian cancer: a case study, Fifteenth IEEE Symposium on Computer-Based Medical Systems (CBMS 2002), June 3-7, Maribor, Slovenia, pp 282-287

10. P. Antal, P. Glenisson, G. Fannes, Y. Moreau, B. De Moor: On the potential of domain literature for clustering and Bayesian network learning, The Eighth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (ACM SIGKDD), 2002, Edmonton, pp 405-414

11. P. Antal, G. Fannes, Y. Moreau, B. De Moor: Using Domain Literature and Data to Annotate and Learn Bayesian Networks, 14th Belgian-Dutch Conference on Artificial Intelligence (BNAIC'02), Leuven, 2002, pp 3-10

12. P. Glenisson, P. Antal, J. Mathys, Y. Moreau and B. De Moor: Evaluation of the vector space representation in text-based gene clustering, Pacific Symposium on Biocomputing (PSB03), Hawaii, 2003, pp 391-402

13. P.Antal, A.Millinghoffer: Learning causal bayesian networks from literature data, Proceedings of the 3rd International Conference on Global Research and Education, Inter-Academia'04, Budapest, 2004, pages 149--160,

14. P.Antal, A.Millinghoffer: A probabilistic knowledge base using annotated bayesian network features. In Proceedings of the 6th International Symposium of Hungarian Researchers on Computational Intelligence, Budapest, 2005, pages 1--12.

15. P. Antal, A. Millinghoffer: Literature mining using Bayesian networks. In Proc. of Third European Workshop on Probabilistic Graphical Models, Prague, 2006. pp 17-24

16. P. Antal, A. Millinghoffer: Learning complex Bayesian network features for classification. In Proc. of Third European Workshop on Probabilistic Graphical Models, Prague, 2006. pp 9-16

17. Millinghoffer, G. Hullám, P. Antal: On inferring the most probable sentences in Bayesian logic, in Working Notes of the Workshop on Intelligent Data Analysis in bioMedicine And Pharmacology (IDAMAP07), the European Conference on Artificial Intelligence in Medicine (AIME'07), 11th European Conference on Artificial Intelligence in Medicine, AIME'07, July 7, 2007, Amsterdam, pp 13-18

18. Millinghoffer, G. Hullám, P. Antal: A probabilistic logic incorporating posteriors of hierarchic graphical models, in Working Notes of The Third Workshop on Combining Probability and Logic (progic07), Sept. 5-7, 2007, Kent, pp –

19. P. Antal, A. Millinghoffer, G. Hullám, Cs. Szalai, A. Falus: A Bayesian View of Challenges in Feature Selection: Feature Aggregation, Multiple Targets, Redundancy and Interaction, ECML/PKDD, Workshop on New challenges for feature selection in data mining and knowledge discovery 2008 (FSDM08), Antwerp, JMLR: Workshop and Conference Proceedings 4, 74-89

20. P Antal, G Hajós, P Sárközy: Bayesian network based analysis in sequential partial genome screening studies, MODGRAPH, June 8., 2009, Nantes, France

21. G. Hullám, P. Antal, Cs. Szalai, A. Falus: Evaluation of methods in GA studies: yet another case for Bayesian network, Machine Learning in System Biology 2009 (MLSB09), Sept 5-6, Ljubljana, Slovenia, Proc. of the Third International Workshop, 35-44