Dr. Martin Reczko, journal publications
1. "Bacterial production and direct functional screening of expanded molecular libraries for discovering inhibitors of protein aggregation" (2019)
D. Delivoria, S. Chia, J. Habchi, M. Perni, I. Matis, N. Papaevgeniou, M. Reczko, N. Chondrogianni, C. Dobson, M. Vendruscolo, G. Skretas
Scientific Advances 2019, 5(10):eaax5108 doi:10.1126/sciadv.aax5108
2. "The future of metabolomics in ELIXIR" (2017)
M. van Rijswijk, C. Beirnaert, C. Caron, M. Cascante, V. Dominguez, W. Dunn, T. Ebbels, F. Giacomoni, A. Gonzalez-Beltran, T. Hankemeier, K. Haug, J. Izquierdo-Garcia, R. Jimenez, F. Jourdan, N. Kale, M. Klapa, O. Kohlbacher, K. Koort, K. Kultima, G. Le Corguille, N. Moschonas, S. Neumann, C. O'Donovan, M. Reczko, P. Rocca-Serra, A. Rosato, R. Salek, S. Sansone, V. Satagopam, D. Schober, R. Shimmo, R. Spicer, O. Spjuth, E. Thevenot, M. Viant, R. Weber, E. Willighagen, G. Zanetti, C. Steinbeck
F1000Research 2017, 6(ELIXIR):1649 doi:10.12688/f1000research.12342.2.
3. "RNA Sequencing Reveals that Kaposi Sarcoma-Associated Herpesvirus Infection Mimics Hypoxia Gene Expression Signature" (2017)
C. Viollet, D. Davis, S. Tekeste, M Reczko, J. Ziegelbauer, F. Pezzella, J. Ragoussis, R. Yarchoan
PLoS Pathogens 13(1): e1006143. doi:10.1371/journal.ppat.1006143
4. "The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species" (2016)
A. Papanicolaou, M. Schetelig, P. Arensburger, P. Atkinson, J. Benoit, K. Bourtzis, P. Castanera, J. Cavanaugh, C. Hsu, C. Childers, I. Curril, H. Dinh, H. Doddapaneni, A. Dolan, S. Dugan, M. Friedrich, G. Gasperi, S. Geib, G. Georgakilas, R. Gibbs, S. Giers, L. Gomulski, M. Gonzalez-Guzman, A. Guillem-Amat, Y. Han, A. Hatzigeorgiou, P. Hernandez-Crespo, D. Hughes, J. Jones, D. Karagkouni, P. Koskinioti, S. Lee, A. Malacrida, M. Manni, K. Mathiopoulos, A. Meccariello, S. Murali, T. Murphy, D. Muzny, G. Oberhofer, F. Ortego, M. Paraskevopoulou, M. Poelchau, J. Qu, M. Reczko, H. Robertson, A. Rosendale, A. Rosselot, G. Saccone, M. Salvemini, G. Savini, P. Schreiner, F. Scolari, P. Siciliano, S. Sim, G. Tsiamis, E. Urena, I. Vlachos, J. Werren, E. Wimmer, K. Worley, A. Zacharopoulou, A. Richards, A. Handler
Genome Biol. 17:192 doi:10.1186/s13059-016-1049-2
5. "A Positive Regulatory Loop between a Wnt-Regulated Non-coding RNA and ASCL2 Controls Intestinal Stem Cell Fate" (2016)
A. Giakountis, P. Moulos, V. Zarkou, C. Oikonomou, V. Harokopos, A. Hatzigeorgiou, M. Reczko, P. Hatzis
Cell Rep. 15(12):2588-96. doi:10.1016/j.celrep.2016.05.038.
6. "Next-Generation Sequencing Analysis Reveals Differential Expression Profiles of MiRNA-mRNA Target Pairs in KSHV-Infected Cells" (2015)
C. Viollet, D. Davis, M Reczko, J. Ziegelbauer, F. Pezzella, J. Ragoussis, R. Yarchoan
PLoS ONE 10(5): e0126439. doi:10.1371/journal.pone.0126439.
7. "The molecular biology of the olive fly comes of age" (2014)
E. Sagri, M. Reczko, K. Tsoumani, M. Gregoriou, V. Harokopos, A. Mavridou, S. Tastsoglou, K. Athanasiadis, J. Ragoussis, K. Mathiopoulos
BMC Genetics 15 (Suppl 2), S8 doi:10.1186/1471-2156-15-S2-S8
8. "Neuroprotection requires the functions of the RNA-binding protein HuR" (2014)
A. Skliris, O. Papadaki, P. Kafasla, I. Karakasiliotis, O. Hazapis, M. Reczko, S. Grammenoudi, J. Bauer, D. Kontoyiannis
Cell Death and Differentiation 22:703–718 doi:10.1038/cdd.2014.158
9. "Olive fly transcriptomics analysis unveils mechanisms of spinosad resistance" (2014)
E. Sagri, M. Reczko, M. Gregoriou, K. Tsoumani, N. Zygouridis, K. Salpea, F. Zalom, J. Ragoussis, K. Mathiopoulos
Olive fly transcriptomics analysis implicates energy metabolism genes in spinosad resistance.
BMC Genomics 15 (1), 714 doi:10.1186/1471-2164-15-714.
10. "Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia" (2014)
C. Camps, H. Saini, D. Mole, H. Choudhry, M. Reczko, J. Guerra-Assunção, Y. Tian, F. Buffa, A. Harris, A. Hatzigeorgiou, A. Enright, J. Ragoussis
Molecular Cancer 13 (1), 28 doi:10.1186/1476-4598-13-28.
11. "DIANA-microT web server v5. 0: service integration into miRNA functional analysis workflows" (2013)
M. Paraskevopoulou, G. Georgakilas, N. Kostoulas, I. Vlachos, T. Vergoulis, M. Reczko, C. Filippidis, T. Dalamagas, A. Hatzigeorgiou
Nucleic Acids Research 41 (W1), W169-W173 doi:10.1093/nar/gkt393.
12. "Identification of microRNA-221/222 and microRNA-323-3p association with rheumatoid arthritis via predictions using the human tumour necrosis factor transgenic mouse model" (2012)
I. Pandis, C. Ospelt, N. Karagianni, M. Denis, M. Reczko, C. Camps, A. Hatzigeorgiou, J. Ragoussis, S. Gay, G. Kollias
Annals of the Rheumatic Diseases 71 (10), 1716-1723 doi:10.1136/annrheumdis-2011-200803.
13. "DIANA miRPath v. 2.0: investigating the combinatorial effect of microRNAs in pathways" (2012)
I. Vlachos, N. Kostoulas, T. Vergoulis, G. Georgakilas, M. Reczko, M. Maragkakis, M. Paraskevopoulou, K. Prionidis, T. Dalamagas, A. Hatzigeorgiou
Nucleic Acids Research 40 (W1), W498-W504 doi:10.1093/nar/gks494.
14. "DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs" (2012)
M. Paraskevopoulou, G. Georgakilas, N. Kostoulas, M. Reczko, M. Maragkakis, T. Dalamagas, A. Hatzigeorgiou
Nucleic Acids Res. 41(Database issue):D239-45 doi:10.1093/nar/gks1246
15. "The Effect of Smoke Combined with the Multicancer Marker, Rs6983267, Located at Region 3 of Chromosome 8q24 in Prostate Cancer Patients" (2012)
A. Papanikolopoulou, O. Landt, M. Reczko, K. Ntoumas, S. Bolomitis, S. I. Tyritzis, C. Konstantinides, N. Drakoulis
Metabolomics 2:1-7. doi:10.4172/2153-0769.1000106
16. "Functional microRNA targets in protein coding sequences" (2012)
M. Reczko, M. Maragkakis, P. Alexiou, I. Grosse, A. Hatzigeorgiou
Bioinformatics. 28:771-6 doi:10.1093/bioinformatics/bts043
17. "Use of mutagenesis, genetic mapping and next generation transcriptomics to investigate insecticide oresistance mechanisms" (2012)
P. Kalajdzic, S. Oehler, M. Reczko, N. Pavlidi, J. Vontas, A. Hatzigeorgiou, C. Savakis
PLoS One. 2012;7(6):e40296. doi:10.1371/journal.pone.0040296.
18. "Accurate microRNA target prediction using detailed binding site accessibility and machine learning on proteomics data" (2011)
M. Reczko, M. Maragkakis, P. Alexiou, G. Papadopoulos and A. Hatzigeorgiou.
Front. Gene., doi: 10.3389/fgene.2011.00103 doi:10.3389/fgene.2011.00103.
19. "TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support" (2012)
T . Vergoulis, I. Vlachos, P. Alexiou, G. Georgakilas, M. Maragkakis, M. Reczko, S. Gerangelos, N. Koziris, T. Dalamagas, A. Hatzigeorgiou
Nucleic Acids Res. 40(Database issue):D222-9. doi:10.1093/nar/gkr1161
20. "A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities" (2011)
E. Tzamali, P. Poirazi, I. Tollis, M. Reczko
BMC Systems Biology 2011, 5:167 doi:10.1186/1752-0509-5-167.
21. "Polymorphisms of the NRAMP1 gene: distribution and susceptibility to the development of pulmonary tuberculosis in the Greek population" (2011)
M. Stagas, G. Papaetis, D. Orphanidou, C. Kostopoulos, S. Syriou, M. Reczko, N. Drakoulis
Medical Science Monitor 2011 Jan;17(1):PH1-6. doi:10.12659/msm.881312.
22. "DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association" (2011)
M. Maragkakis, T. Vergoulis, P. Alexiou, M. Reczko, K. Plomaritou, M. Gousis, K. Kourtis, N. Koziris, T. Dalamagas, A. Hatzigeorgiou
Nucl. Acids Res. 39(suppl 2): W145-W148 doi:10.1093/nar/gkr294
23. "Association study of rs6983267 at 8q24 with prostate cancer in the greek population" (2010)
N. Drakoulis, A. Papanikolopoulou, O. Landt, M. Reczko
European Journal of Oncology Pharmacy, 4(2), 12-13. EID:2-s2.0-77954404655
24. "Encoding of spatio-temporal input characteristics by a CA1 pyramidal neuron model." (2010)
E. Pissadaki, K. Sidiropoulou, M. Reczko, P. Poirazi doi:10.1371/journal.pcbi.1001038
PLoS Computational Biology, 6(12)
25. "Association of the eNOS E298D polymorphism and the risk of myocardial infarction in the greek population" (2010)
C. Dafni, N. Drakoulis, O. Landt, D. Panidis, M. Reczko, D. Cokkinos
BMC Medical Genetics, 11(1) doi:10.1186/1471-2350-11-133
26. "Computational classification of microRNAs in next-generation sequencing data" (2010)
J. Riback, A. Hatzigeorgiou, M. Reczko
Theoretical Chemistry Accounts, 125(3-6), 637-642. doi:10.1007/s00214-009-0684-z
27. "Lost in translation: an assessment and perspective for computational microRNA target identification" (2009)
P. Alexiou P, M. Maragkakis, G.L. Papadopoulos, M. Reczko, A. Hatzigeorgiou
Bioinformatics 25:3049-3055. doi:10.1093/bioinformatics/btp565.
28. "Accurate microRNA target prediction correlates with protein repression levels" (2009)
M. Maragkakis, P. Alexiou, G. Papadopoulos, M. Reczko, T. Dalamagas, G. Giannopoulos, G. Goumas, E. Koukis, K. Kourtis, V. Simossis, P. Sethupathy, T. Vergoulis, N. Koziris, T. Sellis, P. Tsanakas, A. Hatzigeorgiou
BMC Bioinformatics 10:295 doi:10.1186/1471-2105-10-295.
29. "DIANA-mirPath: Integrating human and mouse microRNAs in pathways" (2009)
G. Papadopoulos ,P. Alexiou , M. Maragkakis, M. Reczko, A. Hatzigeorgiou
Bioinformatics 25:1991-3. doi:10.1093/bioinformatics/btp299.
30. "Computational Identification of Bacterial Communities" (2009)
E. Tzamali, P. Poirazi, I. Tollis, M. Reczko
International Journal of Biological and Life Sciences 1(4):185-191.
31. "DIANA-microT web server: elucidating microRNA functions through target prediction" (2009)
M. Maragkakis, M. Reczko, V.A. Simossis, P. Alexiou, G.L. Papadopoulos, T. Dalamagas,
G. Giannopoulos, G. Goumas, E. Koukis, K. Kourtis, T. Vergoulis, N. Koziris, T. Sellis, P. Tsanakas , A. Hatzigeorgiou
Nucleic Acids Res. 37:W273-6.
32. "The database of experimentally supported targets: a functional update of TarBase" (2009)
G. Papadopoulos, M. Reczko, V. Simossis, P. Sethupathy, A. Hatzigeorgiou
Nucleic Acids Res. 37:D155-8.
33. "Prediction of novel microRNA genes in cancer-associated genomic regions: a combined computational and experimental approach" (2009)
A. Oulas, A. Boutla, K. Gkirtzou, M. Reczko, K. Kalantidis, P. Poirazi
Nucleic Acids Res. 37(10), 3276–3287.
34. "MicroRNAs and Cancer: The Search Begins!" (2009)
A. Oulas, M. Reczko, P. Poirazi
IEEE Transactions on Information Technology in Biomedicine, 13:67 - 77.
35. "Discrete clusters of viral encoded miRNAs are associated with complementary strands of the genome and the 7.2-kb stable intron in murine cytomegalovirus" (2007)
A. Buck, J. Santoyo-Lopez, K. Robertson, D. Kumar, M. Reczko, P. Ghazal
Journal of Virology, 81, pp. 13761-13770.
36. "Bidirectional Long Short Term Memory Networks for Predicting the Subcellular Localization of Eukaryotic Proteins" (2006)
T. Thireou, M. Reczko
IEEE Transactions on Computational Biology and Bioinformatics, 4(3), pp.441-6.
37. "Visualization of Functional Aspects of microRNA Regulatory Networks Using the Gene Ontology" (2006)
A. Symeonidis, I. Tollis, M. Reczko
Lecture Notes in Computer Science, Vol. 4345, pp. 13-24.
38. "Using Treemaps to Visualize Phylogenetic Trees" (2005)
A. Arvelakis, M. Reczko, A. Stamatakis, A. Symeonidis and I. Tollis
Lecture Notes in Computer Science, Vol. 3745, pp. 283 - 293 .
39. "Prediction of Subcellular Localization of Eukaryotic Proteins Using Sequence Signals and Composition" (2004)
M. Reczko and A. Hatzigeorgiou
PROTEOMICS 4(6), pp. 1591-1596.
40. "Finding Signal Peptides in human Protein Sequences using Recurrent Neural Networks" (2002)
M. Reczko, E. Staub, P. Fiziev and A. Hatzigeorgiou
Lecture Notes in Computer Science, Springer, Volume 2452, pp. 60-67.
40. "DIANA-EST: a statistical analysis" (2001)
A. Hatzigeorgiou, P. Fiziev and M. Reczko
Bioinformatics 17(10), pp. 913-191.
42. "Improved MR image reconstruction from sparsely sampled scans based on neural networks" (2001)
M. Reczko, D.A. Karras, B.G. Mertzios, D. Graveron-Demilly and D. Van Ormondt.
Pattern Recognition Letters 22, pp. 35-46.
43. "Prediction of human translational initiation sites using a multiple neural network approach" (2000)
C. Derst, M. Reczko and A. Hatzigeorgiou.
Int. J. Comput. Syst. Signals 1(2), pp.169-179.
44. "Neural Networks in MR Image Estimation from Sparsely Sampled Scans" (1999)
M. Reczko, D. A. Karras, B.G. Mertzios, D. Graveron-Demilly and D. van Ormondt
Lecture Notes in Artificial Intelligence 1715, Springer, pp. 75-86.
45. "Prediction of protein hydration sites from sequence by modualar neural networks" (1998)
L. Ehrlich, M. Reczko, H. Bohr and R. Wade.
Protein Engineering, Vol. 11, pp. 11-19.
46. "An update of the DEF database of protein fold class predictions" (1997)
M. Reczko, D. Karras and H. Bohr.
Nucleic Acid Research, Vol. 25, p. 235.
47. "Prediction of Hypervariable CDR-H3 Loop Structures in Antibodies" (1995)
M. Reczko, A.C.R. Martin, H. Bohr and S. Suhai.
Protein Engineering, Vol. 8, (4), pp. 389-395.
48. "A Parallel Neural Network Simulator on the Connection Machine CM-5" (1995)
M. Reczko, A. Hatzigeorgiou, N. Mache, A. Zell and S. Suhai.
CABIOS, vol. 11, pp. 309-315.
49. "The DEF Data Base of Sequence Based Protein Fold Class Prediction" (1994)
M. Reczko and H. Bohr.
Nucleic Acid Research, Vol. 22, pp. 3616-3619.
50. "Protein Secondary Structure Prediction with Partial Recurrent Neural Networks" (1993)
M. Reczko.
SAR and QSAR in Environmental Research, Vol. 1, pp. 153-159.