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1.

001-es BibID:	BIBFORM075319
035-os BibID:	(WoS)000473691900004 (Scopus)85067353429
Első szerző:	Budis, Jaroslav
Cím:	Combining count- and length-based z-scores leads to improved predictions in non-invasive prenatal testing / Budis Jaroslav, Gazdarica Juraj, Radvanszky Jan, Szucs Gabor, Kucharik Marcel, Strieskova Lucia, Gazdaricova Iveta, Harsanyova Maria, Duris Frantisek, Minarik Gabriel, Sekelska Martina, Nagy Balint, Turna Jan, Szemes Tomas
Dátum:	2019
ISSN:	1367-4803
Megjegyzések:	Motivation: Non-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specificity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test. Results: We propose a supplementary method to traditional z-scores to reduce the number of such uninformative calls. The method is based on a novel analysis of the length profile of circulating cell free DNA which compares the change in such profiles when random-based and length-based elimination of some fragments is performed. The proposed method is not as accurate as the standard z-score; however, our results suggest that combination of these two independent methods correctly resolves a substantial portion of healthy samples with an uninformative result. Additionally, we discuss how the proposed method can be used to identify maternal aberrations, thus reducing the risk of false positive and false negative calls. Availability: The open-source code of the proposed methods, together with test data, is freely available for non-commercial users at github web page https://github.com/jbudis/lambda.
Tárgyszavak:	Orvostudományok Klinikai orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk non-invasive prenatal testing improved
Megjelenés:	Bioinformatics. - 35 : 8 (2019), p. 1284-1291. -
További szerzők:	Gazdarica, Juraj Radvanszky, Jan Szűcs Gábor Kucharik, Marcel Strieskova, Lucia Gazdaricova, Iveta Harsanyova, Maria Duris, Frantisek Minarik, Gabriel Sekelska, Martina Nagy Bálint (1956-) (molekuláris genetikus) Turna, Jan Szemes, Tomas (1980-) (biológus)
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
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2.

001-es BibID:	BIBFORM079797
035-os BibID:	(cikkazonosító)398 (WoS)000475910500002 (Scopus)85069472612
Első szerző:	Csősz Éva (biokémikus, molekuláris biológus)
Cím:	Analysis of networks of host proteins in the early time points following HIV transduction / Éva Csősz, Ferenc Tóth, Mohamed Mahdi, George Tsaprailis, Miklós Emri, József Tőzsér
Dátum:	2019
ISSN:	1471-2105
Megjegyzések:	Background: Utilization of quantitative proteomics data on the network level is still a challenge in proteomics data analysis. Currently existing models use sophisticated, sometimes hard to implement analysis techniques. Our aim was to generate a relatively simple strategy for quantitative proteomics data analysis in order to utilize as much of the data generated in a proteomics experiment as possible. Results: In this study, we applied label-free proteomics, and generated a network model utilizing both qualitative, and quantitative data, in order to examine the early host response to Human Immunodeficiency Virus type 1 (HIV-1). A weighted network model was generated based on the amount of proteins measured by mass spectrometry, and analysis of weighted networks and functional sub-networks revealed upregulation of proteins involved in translation, transcription, and DNA condensation in the early phase of the viral life-cycle. Conclusion: A relatively simple strategy for network analysis was created and applied to examine the effect of HIV-1 on host cellular proteome. We believe that our model may prove beneficial in creating algorithms, allowing for both quantitative and qualitative studies of proteome change in various biological and pathological processes by quantitative mass spectrometry.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk weighted network quantitative proteomics host response HIV-1
Megjelenés:	Bmc Bioinformatics. - 20 (2019), p. 1-18. -
További szerzők:	Tóth Ferenc (1980-) (molekuláris biológus) Mahdi, Mohamed (1979-) (orvos, tudományos segédmunkatárs) Tsaprailis, George Emri Miklós (1962-) (fizikus) Tőzsér József (1959-) (molekuláris biológus, biokémikus, vegyész)
Pályázati támogatás:	GINOP-2.3.3-15-2016-00020 GINOP Bolyai János Kutatói Ösztöndíj MTA Felsőoktatási Intézményi Kiválósági Program Egyéb NKFI-6, 125238 Egyéb NIEHS - ES06694 Egyéb NIH/NCI - CA023074 Egyéb NIH/NCRR - 1S10 RR028868-01 Egyéb
Internet cím:	Intézményi repozitóriumban (DEA) tárolt változat DOI
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3.

001-es BibID:	BIBFORM040670
Első szerző:	Mahalingam, Bhuvaneshwari
Cím:	Combining mutations in HIV-1 protease to understand mechanisms of resistance / Mahalingam Bhuvaneshwari, Boross Peter, Wang Yuan-Fang, Louis John M., Fischer Christopher C., Tozser Jozsef, Harrison Robert W., Weber Irene T.
Dátum:	2002
ISSN:	0887-3585
Megjegyzések:	HIV-1 develops resistance to protease inhibitors predominantly by selecting mutations in the protease gene. Studies of resistant mutants of HIV-1 protease with single amino acid substitutions have shown a range of independent effects on specificity, inhibition, and stability. Four double mutants, K45I/L90M, K45I/V82S, D30N/V82S, and N88D/L90M were selected for analysis on the basis of observations of increased or decreased stability or enzymatic activity for the respective single mutants. The double mutants were assayed for catalysis, inhibition, and stability. Crystal structures were analyzed for the double mutants at resolutions of 2.2-1.2 A to determine the associated molecular changes. Sequence-dependent changes in protease-inhibitor interactions were observed in the crystal structures. Mutations D30N, K45I, and V82S showed altered interactions with inhibitor residues at P2/P2', P3/P3'/P4/P4', and P1/P1', respectively. One of the conformations of Met90 in K45I/L90M has an unfavorably close contact with the carbonyl oxygen of Asp25, as observed previously in the L90M single mutant. The observed catalytic efficiency and inhibition for the double mutants depended on the specific substrate or inhibitor. In particular, large variation in cleavage of p6(pol)-PR substrate was observed, which is likely to result in defects in the maturation of the protease from the Gag-Pol precursor and hence viral replication. Three of the double mutants showed values for stability that were intermediate between the values observed for the respective single mutants. D30N/V82S mutant showed lower stability than either of the two individual mutations, which is possibly due to concerted changes in the central P2-P2' and S2-S2' sites. The complex effects of combining mutations are discussed.
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
Megjelenés:	Proteins-Structure Function And Bioinformatics. - 48 : 1 (2002), p. 107-116. -
További szerzők:	Boross Péter (1972-) (biokémikus, vegyész) Wang, Yuan-Fang Louis, John M. Fischer, Christopher C. Tőzsér József (1959-) (molekuláris biológus, biokémikus, vegyész) Harrison, Robert W. Weber, Irene T.
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
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4.

001-es BibID:	BIBFORM050899
035-os BibID:	PMID:24044430 Article ID: 275
Első szerző:	Mótyán János András (biokémikus, molekuláris biológus)
Cím:	A molecular model of the full-length human NOD-like receptor family CARD domain containing 5 (NLRC5) protein / János András Mótyán, Péter Bagossi, Szilvia Benkő, József Tőzsér
Dátum:	2013
ISSN:	1471-2105
Megjegyzések:	Pattern recognition receptors of the immune system have key roles in the regulation of pathways after the recognition of microbial- and danger-associated molecular patterns in vertebrates. Members of NOD-like receptor (NLR) family typically function intracellularly. The NOD-like receptor family CARD domain containing 5 (NLRC5) is the largest member of this family that also contains the largest number of leucine-rich repeats (LRRs).Due to the lack of crystal structures of full-length NLRs, projects have been initiated with the aim to model certain or all members of the family, but systematic studies did not model the full-length NLRC5 due to its unique domain architecture.Our aim was to analyze the LRR sequences of NLRC5 and some NLRC5-related proteins and to build a model for the full-length human NLRC5 by homology modeling. RESULTS: LRR sequences of NLRC5 were aligned and were compared with the consensus pattern of ribonuclease inhibitor protein (RI)-like LRR subfamily. Two types of alternating consensus patterns previously identified for RI repeats were also found in NLRC5. A homology model for full-length human NLRC5 was prepared and, besides the closed conformation of monomeric NLRC5, a heptameric platform was also modeled for the opened conformational NLRC5 monomers. CONCLUSIONS: Identification of consensus patterns of leucine-rich repeat sequences helped to identify LRRs in NLRC5 and to predict their number and position within the protein. In spite of the lack of fully adequate template structures, the presence of an untypical CARD domain and unusually high number of LRRs in NLRC5, we were able to construct a homology model for both the monomeric and homo-heptameric full-length human NLRC5 protein.
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban NLRC5 Molecular modeling LRR protein NOD-like receptor
Megjelenés:	BMC Bioinformatics 14 : 1 (2013), p. 1-11. -
További szerzők:	Bagossi Péter (1966-2011) (biokémikus, vegyész) Benkő Szilvia (1973-) (molekuláris biológus) Tőzsér József (1959-) (molekuláris biológus, biokémikus, vegyész)
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
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5.

001-es BibID:	BIBFORM003489
035-os BibID:	(scopus)54549105754 (wos)000260487500001
Első szerző:	Roszik János (biofizikus)
Cím:	AccPbFRET : an ImageJ plugin for semi-automatic, fully corrected analysis of acceptor photobleaching FRET images / Roszik János, Szöllősi János, Vereb György
Dátum:	2008
Megjegyzések:	The acceptor photobleaching fluorescence resonance energy transfer (FRET) method is widely used for monitoring molecular interactions in cells. This method of FRET, while among those with the simplest mathematics, is robust, self-controlled and independent of fluorophore amounts and ratios. RESULTS: AccPbFRET is a user-friendly, efficient ImageJ plugin which allows fully corrected, pixel-wise calculation and detailed, ROI (region of interest)-based analysis of FRET efficiencies in microscopic images. Furthermore, automatic registration and semi-automatic analysis of large image sets is provided, which are not available in any existing FRET evaluation software. CONCLUSIONS: Despite of the widespread applicability of the acceptor photobleaching FRET technique, this is the first paper where all possible sources of major errors of the measurement and analysis are considered, and AccPbFRET is the only program which provides the complete suite of corrections - for registering image pairs, for unwanted photobleaching of the donor, for cross-talk of the acceptor and/or its photoproduct to the donor channel and for partial photobleaching of the acceptor. The program efficiently speeds up the analysis of large image sets even for novice users and is freely available.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk acceptor photobleaching FRET CLSM software
Megjelenés:	BMC Bioinformatics. - 9 : 1 (2008), p. 346. -
További szerzők:	Szöllősi János (1953-) (biofizikus) Vereb György (1965-) (biofizikus, orvos)
Internet cím:	elektronikus változat DOI elektronikus változat
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6.

001-es BibID:	BIBFORM116513
035-os BibID:	(Scopus)85173464630 (WOS)001077676500001
Első szerző:	Sanches, Karoline
Cím:	Structure-function relationships in domain peptides : from the sea anemone / Sanches Karoline, Ashwood Lauren M., Olushola-Siedoks Abisola Ave-Maria, Wai Dorothy C. C., Rahman Arfatur, Shakeel Kashmala, Naseem Muhammad Umair, Panyi Gyorgy, Prentis Peter J., Norton Raymond S.
Dátum:	2024
ISSN:	0887-3585
Megjegyzések:	Diverse structural scaffolds have been described in peptides from sea anemones, with the ShKT domain being a common scaffold first identified in ShK toxin from Stichodactyla helianthus. ShK is a potent blocker of voltage-gated potassium channels (KV1.x), and an analog, ShK-186 (dalazatide), has completed Phase 1 clinical trials in plaque psoriasis. The ShKT domain has been found in numerous other species, but only a tiny fraction of ShKT domains has been characterized functionally. Despite adopting the canonical ShK fold, some ShKT peptides from sea anemones inhibit KV1.x, while others do not. Mutagenesis studies have shown that a Lys-Tyr (KY) dyad plays a key role in KV1.x blockade, although a cationic residue followed by a hydrophobic residue may also suffice. Nevertheless, ShKT peptides displaying an ShK-like fold and containing a KY dyad do not necessarily block potassium channels, so additional criteria are needed to determine whether new ShKT peptides might show activity against potassium channels. In this study, we used a combination of NMR and molecular dynamics (MD) simulations to assess the potential activity of a new ShKT peptide. We determined the structure of ShKT-Ts1, from the sea anemone Telmatactis stephensoni, examined its tissue localization, and investigated its activity against a range of ion channels. As ShKT-Ts1 showed no activity against KV1.x channels, we used MD simulations to investigate whether solvent exposure of the dyad residues may be informative in rationalizing and potentially predicting the ability of ShKT peptides to block KV1.x channels. We show that either a buried dyad that does not become exposed during MD simulations, or a partially exposed dyad that becomes buried during MD simulations, correlates with weak or absent activity against KV1.x channels. Therefore, structure determination coupled with MD simulations, may be used to predict whether new sequences belonging to the ShKT family may act as potassium channel blockers.
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk molecular dynamics NMR peptide potassium channel sea anemone ShKT domain structure determination
Megjelenés:	Proteins-Structure Function And Bioinformatics. - 92 : 2 (2023), p. 192-205. -
További szerzők:	Ashwood, Lauren M. Olushola-Siedoks, Abisola Ave-Maria Wai, Dorothy C. C. Rahman, Arfatur Shakeel, Kashmala Naseem, Muhammad Umair (1993-) (biofizikus, molekuláris biológus) Panyi György (1966-) (biofizikus) Prentis, Peter Norton, Raymond S.
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
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7.

001-es BibID:	BIBFORM018163
Első szerző:	Sebestyén Endre
Cím:	DoOPSearch : a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes / Sebestyén Endre, Nagy Tibor, Suhai Sándor, Barta Endre
Dátum:	2009
ISSN:	1471-2105
Megjegyzések:	The comparative genomic analysis of a large number of orthologous promoter regions of the chordate and plant genes from the DoOP databases shows thousands of conserved motifs. Most of these motifs differ from any known transcription factor binding site (TFBS). To identify common conserved motifs, we need a specific tool to be able to search amongst them. Since conserved motifs from the DoOP databases are linked to genes, the result of such a search can give a list of genes that are potentially regulated by the same transcription factor(s). Results We have developed a new tool called DoOPSearch http://doopsearch.abc.hu webcite for the analysis of the conserved motifs in the promoter regions of chordate or plant genes. We used the orthologous promoters of the DoOP database to extract thousands of conserved motifs from different taxonomic groups. The advantage of this approach is that different sets of conserved motifs might be found depending on how broad the taxonomic coverage of the underlying orthologous promoter sequence collection is (consider e.g. primates vs. mammals or Brassicaceae vs. Viridiplantae). The DoOPSearch tool allows the users to search these motif collections or the promoter regions of DoOP with user supplied query sequences or any of the conserved motifs from the DoOP database. To find overrepresented gene ontologies, the gene lists obtained can be analysed further using a modified version of the GeneMerge program. Conclusion We present here a comparative genomics based promoter analysis tool. Our system is based on a unique collection of conserved promoter motifs characteristic of different taxonomic groups. We offer both a command line and a web-based tool for searching in these motif collections using user specified queries. These can be either short promoter sequences or consensus sequences of known transcription factor binding sites. The GeneMerge analysis of the search results allows the user to identify statistically overrepresented Gene Ontology terms that might provide a clue on the function of the motifs and genes.
Tárgyszavak:	Orvostudományok Elméleti orvostudományok konferenciacikk
Megjelenés:	Bmc Bioinformatics [electronic resource]. - 10 : Suppl.6. (2009), p. S6. -
További szerzők:	Nagy Tibor (Gödöllő) Suhai Sándor Barta Endre (1963-) (molekuláris biológus)
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
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8.

001-es BibID:	BIBFORM002428
Első szerző:	Thallinger, Gerhard G.
Cím:	TAMEE : data management and analysis for tissue microarrays / Thallinger G. G., Baumgartner K., Pirklbauer M., Uray M., Pauritsch E., Méhes G., Buck C. R., Zatloukal K., Trajanoski Z.
Dátum:	2007
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban külföldön készült közlemény
Megjelenés:	BMC Bioinformatics 8 (2007), p. 81-92. -
További szerzők:	Baumgartner, Kerstin Pirklbauer, Martin Uray, Martina Pauritsch, Elke Méhes Gábor (1966-) (patológus) Buck, Charles R. Zatloukal, Kurt Trajanoski, Zlatko
Internet cím:	elektronikus változat DOI
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