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1.

001-es BibID:BIBFORM104602
035-os BibID:(Scopus)85141858760 (WOS)000894561800002
Első szerző:Bácsi Attila (immunológus)
Cím:Whole blood transcriptome characterization of young female triathlon athletes following an endurance exercise : a pilot study / Bácsi Attila, Penyige András, Becs Gergely, Benkő Szilvia, Kovács Elek Gergő, Jenei Csaba, Pócsi István, Balla József, Csernoch László, Balatoni Ildikó
Dátum:2022
ISSN:1094-8341
Megjegyzések:The vast majority of studies focusing on the effects of endurance exercise on hematological parameters and leukocyte gene expression were performed in adult men, so our aim was to investigate these changes in young females. Four young (age 15.3 ? 1.3 years) elite female athletes completed an exercise session, in which they accomplished the cycling and running disciplines of a junior triathlon race. Blood samples were taken immediately before the exercise, right after the exercise, and then 1, 2, and 7 days later. Analysis of cell counts and routine biochemical parameters was complemented by RNA sequencing (RNA-seq) to whole blood samples. The applied exercise load did not trigger remarkable changes in either cardiovascular or biochemical parameters; however, it caused a significant increase in the percentage of neutrophils and a significant reduction in the ratio of lymphocytes immediately after exercise. Furthermore, endurance exercise induced a characteristic gene expression pattern change in the blood transcriptome. Gene set enrichment analysis (GSEA) using the Reactome database revealed that the expression of genes involved in immune processes and neutrophil granulocyte activation was upregulated, while the expression of genes important in translation and rRNA metabolism was downregulated. Comparison of a set of immune cell gene signatures (ImSig) and our transcriptomic data identified 15 overlapping genes related to T cell functions, and involved in podosome formation and adhesion to the vessel wall. Our results suggest that RNA-seq to whole blood together with ImSig analysis are useful tools for investigation of systemic responses to endurance exercise.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
ImSig
RNA sequencing
endurance exercise
whole blood transcriptome
young female athletes
Megjelenés:Physiological Genomics. - 54 : 11 (2022), p. 457-469. -
További szerzők:Penyige András (1954-) (molekuláris genetikus) Becs Gergely Benkő Szilvia (1973-) (molekuláris biológus) Kovács Elek Gergő Jenei Csaba (1976-) (kardiológus) Pócsi István (1961-) (vegyész) Balla József (1959-) (belgyógyász, nephrológus) Csernoch László (1961-) (élettanász) Balatoni Ildikó (1970-) (orvos)
Pályázati támogatás:GINOP-2.3.2-15-2016-00062
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2.

001-es BibID:BIBFORM013292
Első szerző:Balázs Anita (molekuláris biológus)
Cím:Atfa bZIP-type transcription factor regulates oxidative and osmotic stress responses in Aspergillus nidulans / Anita Balázs, Imre Pócsi, Zsuzsanna Hamari, Éva Leiter, Tamás Emri, Márton Miskei, Judit Oláh, Viktória Tóth, Nikoletta Hegedűs, Rolf A. Prade, Mónika Molnár, István Pócsi
Dátum:2010
ISSN:1617-4615 1617-4623
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
Megjelenés:Molecular Genetics and Genomics. - 283 : 3 (2010), p. 289-303. -
További szerzők:Pócsi Imre Hamari Zsuzsanna Leiter Éva (1976-) (biológus) Emri Tamás (1969-) (biológus) Miskei Márton (1978-) (molekuláris biológus, genetikus) Oláh Judit Tóth Viktória (1984-) (biológus) Hegedűs Nikoletta Prade, Rolf A. Molnár Mónika Pócsi István (1961-) (vegyész)
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elektronikus változat
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3.

001-es BibID:BIBFORM075079
Első szerző:Bana Nóra Á.
Cím:The red deer Cervus elaphus genome CerEla1.0 : sequencing, annotating, genes, and chromosomes / Nóra Á. Bana, Anna Nyiri, János Nagy, Krisztián Frank, Tibor Nagy, Viktor Stéger, Mátyás Schiller, Péter Lakatos, László Sugár, Péter Horn, Endre Barta, László Orosz
Dátum:2018
ISSN:1617-4615
Megjegyzések:We present here the de novo genome assembly CerEla1.0 for the red deer, Cervus elaphus, an emblematic member of the natural megafauna of the Northern Hemisphere. Humans spread the species in the South. Today, the red deer is also a farm-bred animal and is becoming a model animal in biomedical and population studies. Stag DNA was sequenced at 74x coverage by Illumina technology. The ALLPATHS-LG assembly of the reads resulted in 34.7?x?103 scaffolds, 26.1?x?103 of which were utilized in Cer.Ela1.0. The assembly spans 3.4 Gbp. For building the red deer pseudochromosomes, a pre-established genetic map was used for main anchor points. A nearly complete co-linearity was found between the mapmarker sequences of the deer genetic map and the order and orientation of the orthologous sequences in the syntenic bovine regions. Syntenies were also conserved at the in-scaffold level. The cM distances corresponded to 1.34 Mbp uniformly along the deer genome. Chromosomal rearrangements between deer and cattle were demonstrated. 2.8?x?106 SNPs, 365?x?103 indels and 19368 protein-coding genes were identified in CerEla1.0, along with positions for centromerons. CerEla1.0 demonstrates the utilization of dual references, i.e., when a target genome (here C. elaphus) already has a pre-established genetic map, and is combined with the well-established whole genome sequence of a closely related species (here Bos taurus). Genome-wide association studies (GWAS) that CerEla1.0 (NCBI, MKHE00000000) could serve for are discussed.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
Megjelenés:Molecular Genetics And Genomics. - 293 : 3 (2018), p. 665-684. -
További szerzők:Nyíri Anna Nagy János (Kaposvár) Frank Krisztián Nagy Tibor (Gödöllő) Stéger Viktor Schiller Mátyás Lakatos Péter (belgyógyász) Sugár László Horn Péter (agrár) Barta Endre (1963-) (molekuláris biológus) Orosz László (Budapest)
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4.

001-es BibID:BIBFORM099535
Első szerző:Bartáné Tóth Beáta (molekuláris biológus)
Cím:Regulatory modules of human thermogenic adipocytes : functional genomics of large cohort and Meta-analysis derived marker-genes / B. Tóth Beáta, Barta Zoltán, Barta Ákos Barnabás, Fésüs László
Dátum:2021
ISSN:1471-2164
Megjegyzések:Background Recently, ProFAT and BATLAS studies identified brown and white adipocytes marker genes based on analysis of large databases. They offered scores to determine the thermogenic status of adipocytes using the gene-expression data of these markers. In this work, we investigated the functional context of these genes. Results Gene Set Enrichment Analyses (KEGG, Reactome) of the BATLAS and ProFAT marker-genes identified pathways deterministic in the formation of brown and white adipocytes. The collection of the annotated proteins of the defined pathways resulted in expanded white and brown characteristic protein-sets, which theoretically contain all functional proteins that could be involved in the formation of adipocytes. Based on our previously obtained RNA-seq data, we visualized the expression profile of these proteins coding genes and found patterns consistent with the two adipocyte phenotypes. The trajectory of the regulatory processes could be outlined by the transcriptional profile of progenitor and differentiated adipocytes, highlighting the importance of suppression processes in browning. Protein interaction network-based functional genomics by STRING, Cytoscape and R-Igraph platforms revealed that different biological processes shape the brown and white adipocytes and highlighted key regulatory elements and modules including GAPDH-CS, DECR1, SOD2, IL6, HRAS, MTOR, INS-AKT, ERBB2 and 4-NFKB, and SLIT-ROBO-MAPK. To assess the potential role of a particular protein in shaping adipocytes, we assigned interaction network location-based scores (betweenness centrality, number of bridges) to them and created a freely accessible platform, the AdipoNET (https//adiponet.com), to conveniently use these data. The Eukaryote Promoter Database predicted the response elements in the UCP1 promoter for the identified, potentially important transcription factors (HIF1A, MYC, REL, PPARG, TP53, AR, RUNX, and FoxO1). Conclusion Our integrative approach-based results allowed us to investigate potential regulatory elements of thermogenesis in adipose tissue. The analyses revealed that some unique biological processes form the brown and white adipocyte phenotypes, which presumes the existence of the transitional states. The data also suggests that the two phenotypes are not mutually exclusive, and differentiation of thermogenic adipocyte requires induction of browning as well as repressions of whitening. The recognition of these simultaneous actions and the identified regulatory modules can open new direction in obesity research.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
Megjelenés:BMC Genomics. - 22 : 1 (2021), p. 1-21. -
További szerzők:Barta Zoltán (1967-) (biológus, zoológus) Barta Ákos Barnabás Fésüs László (1947-) (orvos biokémikus)
Pályázati támogatás:GINOP-2.3.2-15-2016-00006
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5.

001-es BibID:BIBFORM054512
Első szerző:Brignull, Louise M.
Cím:Reprogramming of lysosomal gene expression by interleukin-4 and Stat6 / Louise M. Brignull, Zsolt Czimmerer, Hafida Saidi, Bence Daniel, Izabel Villela, Nathan W. Bartlett, Sebastian L. Johnston, Lisiane B. Meira, Laszlo Nagy, Axel Nohturfft
Dátum:2013
ISSN:1471-2164
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
Megjelenés:BMC Genomics [electronic resource]. - 14 : 1 (2013), p. 1-20. -
További szerzők:Czimmerer Zsolt (1981-) (molekuláris biológus) Saidi, Hafida Dániel Bence (1987-) (molekuláris biológus) Villela, Izabel Bartlett, Nathan W. Johnston, Sebastian L. Meira, Lisiane B. Nagy László (1966-) (molekuláris sejtbiológus, biokémikus) Nohturfft, Axel
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6.

001-es BibID:BIBFORM003460
Első szerző:Gombos Katalin
Cím:Characterization of microarray gene expression profiles of early stage thyroid tumours / Katalin Gombos, Eszter Szele, István Kiss, Timea Varjas, László Puskás, László Kozma, Ferenc Juhász, Erik Kovács, István Szanyi, István Ember
Dátum:2007
Megjegyzések:Microarray analysis offers the opportunity of screen ing transcriptional expression ptofile of neoplastic celis on a genomic level. Defining consistent changes in gene expression patrem of tumours enables the deiection of genes essential for tumorigenesis and might provide biomarkers to early recognition of malignant behaviourand new therapeutical targets. Patients and Methods: A high-density oligonucleotide wray with 20,000 human gene-specific oligonucleotide was used to analyze benign and earlYcstage malignant thyroid tumours of epithelial origin: folliatlar adenoma, foliicular carcinoma and papillary carcinoma, compw'ed to normal thyroid tissue. Results: Significant expression dijferences of 279 genes - underexpression of 252 and overexpression of 27 gen es - were found. The overlappinggenes of the different histological types were examined extenSively. Among thesegenes a limited set acting on the same transcriptional path way. through NF-KB; were found. Conc1usion: The role of overlapping genes in histologicaliy different tumours has not been c1arified, but might represent early or pivotaf steps of carcinogenesis. Ali investigated histiotypes of tumourscontciined signijicantly modulated genes acting on the NE-KB regulatOlY pathway. Our findings suggest that modulation of NF-KB signcMling plays a cn/cial role in early thyroid carcínogenesis.
Tárgyszavak:Orvostudományok Klinikai orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
gene expression profiling
thyroid tumour
follicular adenoma
follicular carcinoma
papillary carcinoma
microarray
Megjelenés:Cancer Genomics and Proteomics. - 4 : 6 (2007), p. 403-410. -
További szerzők:Szele Eszter Kiss István (orvos) Varjas Tímea Puskás László Kozma László (orvos) Kovács Erik Szanyi István Ember István Juhász Ferenc (1952-) (sebész)
Internet cím:elektronikus változat
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7.

001-es BibID:BIBFORM066626
Első szerző:Hitre Erika
Cím:Influence of thymidylate synthase gene polymorphisms on the survival of colorectal cancer patients receiving adjuvant 5-fluorouracil / Erika Hitre, Barna Budai, Vilmos Adleff, Ferenc Czeglédi, Zsolt Horváth, Fruzsina Gyergyay, József Lövey, Tibor Kovács, Zsolt Orosz, István Láng, Miklós Kásler, Judit Kralovánszky
Dátum:2005
ISSN:1744-6872
Tárgyszavak:Orvostudományok Klinikai orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
Megjelenés:Pharmacogenetics And Genomics 15 : 10 (2005), p. 723-730. -
További szerzők:Budai Barna Adleff Vilmos Czeglédi Ferenc Horváth Zsolt (1964-) (onkológus, belgyógyász, klinikai farmakológus) Gyergyay Fruzsina Lövey József Kovács Tibor (1973-) (belgyógyász) Orosz Zsolt (1954-) (pathológus) Láng István Kásler Miklós Kralovánszky Judit
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8.

001-es BibID:BIBFORM072517
035-os BibID:(cikkazonosító)158 (WoS)000426305200003 (Scopus)85042425048
Első szerző:Ivády Gergely (laboratóriumi szakorvos)
Cím:Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system / Ivády Gergely, Madar László, Dzsudzsák Erika, Koczok Katalin, Kappelmayer János, Krulisova Veronika, Macek Milan, Horváth Attila, Balogh István
Dátum:2018
ISSN:1471-2164
Megjegyzések:BackgroundCurrent technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have the advantage of delivering long and high quality reads, problems might occur when sequencing homopolymer-containing regions, since the repeating identical bases are going to incorporate during the same synthesis cycle, which leads to uncertainty in base calling. The aim of this study was to evaluate the analytical performance of a pyrosequencing-based next-generation sequencing system in detecting homopolymer sequences using homopolymer-preintegrated plasmid constructs and human DNA samples originating from patients with cystic fibrosis.ResultsIn the plasmid system average correct genotyping was 95.8% in 4-mers, 87.4% in 5-mers and 72.1% in 6-mers. Despite the experienced low genotyping accuracy in 5- and 6-mers, it was possible to generate amplicons with more than a 90% adequate detection rate in every homopolymer tract. When homopolymers in the CFTR gene were sequenced average accuracy was 89.3%, but varied in a wide range (52.2 ? 99.1%). In all but one case, an optimal amplicon-sequencing primer combination could be identified. In that single case (7A tract in exon 14 (c.2046_2052)), none of the tested primer sets produced the required analytical performance.ConclusionsOur results show that pyrosequencing is the most reliable in case of 4-mers and as homopolymer length gradually increases, accuracy deteriorates. With careful primer selection, the NGS system was able to correctly genotype all but one of the homopolymers in the CFTR gene. In conclusion, we configured a plasmid test system that can be used to assess genotyping accuracy of NGS devices and developed an accurate NGS assay for the molecular diagnosis of CF using self-designed primers for amplification and sequencing.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
Pyrosequencing
Homopolymer detection
Cystic fibrosis
Megjelenés:BMC Genomics. - 19 (2018), p. 1-8. -
További szerzők:Madar László (1972-) (klinikai laboratóriumi kutató) Dzsudzsák Erika Koczok Katalin (1979-) (labororvos) Kappelmayer János (1960-) (laboratóriumi szakorvos) Krulisova, Veronika Macek Jr., Milan Horváth Attila (1988-) (programtervező informatikus) Balogh István (1972-) (molekuláris biológus, genetikus)
Pályázati támogatás:K109076
OTKA
GINOP-2.3.2-15-2016-00039
GINOP
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9.

001-es BibID:BIBFORM065115
Első szerző:Nagy Gergely (molekuláris biológus)
Cím:Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA / Gergely Nagy, Erik Czipa, László Steiner, Tibor Nagy, Sándor Pongor, László Nagy, Endre Barta
Dátum:2016
ISSN:1471-2164
Megjegyzések:BACKGROUND:ChIP-seq provides a wealth of information on the approximate location of DNA-binding proteins genome-wide. It is known that the targeted motifs in most cases can be found at the peak centers. A high resolution mapping of ChIP-seq peaks could in principle allow the fine mapping of the protein constituents within protein complexes, but the current ChIP-seq analysis pipelines do not target the basepair resolution strand specific mapping of peak summits.RESULTS:The approach proposed here is based on i) locating regions that are bound by a sufficient number of proteins constituting a complex; ii) determining the position of the underlying motif using either a direct or a de novo motif search approach; and iii) determining the exact location of the peak summits with respect to the binding motif in a strand specific manner. We applied this method for analyzing the CTCF/cohesin complex, which holds together DNA loops. The relative positions of the constituents of the complex were determined with one-basepair estimated accuracy. Mapping the positions on a 3D model of DNA made it possible to deduce the approximate local topology of the complex that allowed us to predict how the CTCF/cohesin complex locks the DNA loops. As the positioning of the proteins was not compatible with previous models of loop closure, we proposed a plausible "double embrace" model in which the DNA loop is held together by two adjacent cohesin rings in such a way that the ring anchored by CTCF to one DNA duplex encircles the other DNA double helix and vice versa.CONCLUSIONS:A motif-centered, strand specific analysis of ChIP-seq data improves the accuracy of determining peak positions. If a genome contains a large number of binding sites for a given protein complex, such as transcription factor heterodimers or transcription factor/cofactor complexes, the relative position of the constituent proteins on the DNA can be established with an accuracy that allow one to deduce the local topology of the protein complex. The proposed high resolution mapping approach of ChIP-seq data is applicable for detecting the contact topology of DNA-binding protein complexes.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
CTCF
DNA loop
cohesin
ChIP-seq
Megjelenés:BMC Genomics. - 17 : 637 (2016), p. 1-9. -
További szerzők:Czipa Erik (1990-) (molekuláris biológus, bioinformatikus) Steiner László Nagy Tibor (Gödöllő) Pongor Sándor Nagy László (1966-) (molekuláris sejtbiológus, biokémikus) Barta Endre (1963-) (molekuláris biológus)
Pályázati támogatás:TÁMOP-4.2.2.C-11/1/KONV-2012-0010
TÁMOP
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10.

001-es BibID:BIBFORM097910
035-os BibID:(cikkazonosító)310
Első szerző:Nagy Nikoletta Andrea (biológus)
Cím:Draft genome of a biparental beetle species, Lethrus apterus / Nagy Nikoletta A., Rácz Rita, Rimington Oliver, Póliska Szilárd, Orozco-terWengel Pablo, Bruford Michael W., Barta Zoltán
Dátum:2021
ISSN:1471-2164
Tárgyszavak:Orvostudományok Klinikai orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
Megjelenés:BMC Genomics. - 22 : 1 (2021). -
További szerzők:Rácz Rita (1989-) (biológus) Rimington, Oliver Póliska Szilárd (1978-) (biológus) Orozco-terWengel, Pablo Bruford, Michael W. Barta Zoltán (1967-) (biológus, zoológus)
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11.

001-es BibID:BIBFORM018108
Első szerző:Pócsi István (vegyész)
Cím:Comparison of gene expression signatures of diamide, H2O2 and menadione exposed Aspergillus nidulans cultures - linking genome-wide transcriptional changes to cellular physiology / István Pócsi, Márton Miskei, Zsolt Karányi, Tamás Emri, Patricia Ayoubi, Tünde Pusztahelyi, György Balla, Rolf A. Prade
Dátum:2005
ISSN:1471-2164
Megjegyzések:Background In addition to their cytotoxic nature, reactive oxygen species (ROS) are also signal molecules in diverse cellular processes in eukaryotic organisms. Linking genome-wide transcriptional changes to cellular physiology in oxidative stress-exposed Aspergillus nidulans cultures provides the opportunity to estimate the sizes of peroxide (O22-), superoxide (O2?-) and glutathione/glutathione disulphide (GSH/GSSG) redox imbalance responses. Results Genome-wide transcriptional changes triggered by diamide, H2O2 and menadione in A. nidulans vegetative tissues were recorded using DNA microarrays containing 3533 unique PCR-amplified probes. Evaluation of LOESS-normalized data indicated that 2499 gene probes were affected by at least one stress-inducing agent. The stress induced by diamide and H2O2 were pulse-like, with recovery after 1 h exposure time while no recovery was observed with menadione. The distribution of stress-responsive gene probes among major physiological functional categories was approximately the same for each agent. The gene group sizes solely responsive to changes in intracellular O22-, O2?- concentrations or to GSH/GSSG redox imbalance were estimated at 7.7, 32.6 and 13.0 %, respectively. Gene groups responsive to diamide, H2O2 and menadione treatments and gene groups influenced by GSH/GSSG, O22- and O2?- were only partly overlapping with distinct enrichment profiles within functional categories. Changes in the GSH/GSSG redox state influenced expression of genes coding for PBS2 like MAPK kinase homologue, PSK2 kinase homologue, AtfA transcription factor, and many elements of ubiquitin tagging, cell division cycle regulators, translation machinery proteins, defense and stress proteins, transport proteins as well as many enzymes of the primary and secondary metabolisms. Meanwhile, a separate set of genes encoding transport proteins, CpcA and JlbA amino acid starvation-responsive transcription factors, and some elements of sexual development and sporulation was ROS responsive. Conclusion The existence of separate O22-, O2?- and GSH/GSSG responsive gene groups in a eukaryotic genome has been demonstrated. Oxidant-triggered, genome-wide transcriptional changes should be analyzed considering changes in oxidative stress-responsive physiological conditions and not correlating them directly to the chemistry and concentrations of the oxidative stress-inducing agent.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
Megjelenés:BMC Genomics. - 6 : 182 (2005), p. 1-18 . -
További szerzők:Miskei Márton (1978-) (molekuláris biológus, genetikus) Karányi Zsolt (1961-) (biostatisztikus, bioinformatikus) Emri Tamás (1969-) (biológus) Ayoubi, Patricia Pusztahelyi Tünde (1969-) (biológus, angol-magyar szakfordító) Balla György (1953-) (csecsemő és gyermekgyógyász, neonatológus) Prade, Rolf A.
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12.

001-es BibID:BIBFORM012859
Első szerző:Stéger Viktor
Cím:Antler development and coupled osteoporosis in the skeleton of red deer cervus elaphus : expression dynamics for regulatory and effector genes / Stéger, V., Molnár, A., Borsy, A., Gyurján, I., Szabolcsi, Z., Dancs, G., Molnár, J., Papp, P., Nagy, J., Puskás, L., Barta, E., Zomborszky, Z., Horn, P., Podani, J., Semsey, S., Lakatos, P., Orosz, L.
Dátum:2010
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
Megjelenés:Molecular Genetics and Genomics. - 284 : 4 (2010), p. 273-287. -
További szerzők:Molnár Andrea (Budapest) Borsy Adrienn Gyurján István Szabolcsi Zoltán Dancs Gábor Molnár János (Gödöllő) Papp Péter (Gödöllő) Nagy János (Kaposvár) Puskás László Barta Endre (1963-) (molekuláris biológus) Zomborszky Zoltán Horn Péter Podani János Semsey Szabolcs Lakatos Péter (belgyógyász) Orosz László (Budapest)
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