János Molnár

• Master of Science
• Bioinformatician at Enviroinvest, Budapest, Hungary

Metagenomics is a helpful tool for the analysis of unculturable organisms and viruses. Viruses that target bacteria and archaea play important roles in the microbial diversity of various ecosystems. Here we show that Methanosarcina virus MV (MetMV), the second Methanosarcina sp. virus with a completely determined genome, is characteristic of hydroc...

Grapevine can be infected by several viruses and viroids, the presence of which can lead to yield losses and vineyard decline. Our previous survey of vineyards in Hungary suggested that viral infection originates from infected propagation material. To investigate whether rootstocks can be a source of virus infections, we surveyed seventeen rootstoc...

Xanthomonas oryzae pv. oryzae is the causative agent of bacterial leaf blight of rice. The application of bacteriophages may provide an effective tool against this bacterium. Here, we report the complete genome sequences of 10 newly isolated OP2-like X. oryzae pv. oryzae bacteriophages.

Fruit trees, such as apricot trees, are constantly exposed to the attack of viruses. As they are propagated in a vegetative way, this risk is present not only in the field, where they remain for decades, but also during their propagation. Metagenomic diagnostic methods, based on next generation sequencing (NGS), offer unique possibilities to reveal...

Woody perennial plants like grapevine and fruit trees can be infected by several viruses even as multiple infections. Since they are propagated vegetatively, the phytosanitary status of the propagation material (both the rootstock and the variety) can have a profound effect on the lifetime and health of the new plantations. The fast evolution of se...

As virus diseases cannot be controlled by traditional plant protection methods, the risk of their spread have to be minimized on vegetatively propagated plants, such as grapevine. Metagenomic approaches used for virus diagnostics offer a unique opportunity to reveal the presence of all viral pathogens in the investigated plant, which is why their a...

The mitogenomes of one animal of each of the three Mangalica breeds, Blonde, Red, and Swallow-belly were assembled from reads obtained by Next Generation Sequencing of the three genomes. Features of the mitogenomes were identical in the three breeds, apart from a second tRNA-Val gene on the L strand in Swallow-belly. Phylogenetic comparison of the...

Background Detection of somatic mutations is one of the main goals of next generation DNA sequencing. A wide range of experimental systems are available for the study of spontaneous or environmentally induced mutagenic processes. However, most of the routinely used mutation calling algorithms are not optimised for the simultaneous analysis of multi...

Background Genomic mutations caused by cytotoxic agents used in cancer chemotherapy may cause secondary malignancies as well as contribute to the evolution of treatment-resistant tumour cells. The stable diploid genome of the chicken DT40 lymphoblast cell line, an established DNA repair model system, is well suited to accurately assay genomic mutat...

Transmembrane protein coding genes are commonly associated with human diseases. We characterized disease causing mutations and natural polymorphisms in transmembrane proteins by mapping missense genetic variations from the UniProt database on the transmembrane protein topology listed in the Human Transmembrane Proteome database. We found characteri...

The significance of the different amino acid substitutions of polymorphisms within distinct topological sites. Tables represent the observed (OBS) values, the average values of random sampling of hundred times (AVG), the standard deviation of the random sampling (STD) and the ratio of the observed minus average and standard deviation values ((OBS-A...

Occurrences of polymorphisms and disease associated mutations in the TM region and the “predictive value” table. Tables represent the counts of occurrences of the specific amino acid changes within the TM region in the case of disease associated mutations and polymorphisms. Additionally there is a worksheet which shows the summarized counts of the...

The significance of the different amino acid substitutions of disease associated mutations within distinct topological sites. Tables represent the observed (OBS) values, the average values of random sampling of hundred times (AVG), the standard deviation of the random sampling (STD) and the ratio of the observed minus average and standard deviation...

Step by step description of preanalysis. A detailed description of the steps which are necessary to reproduce our analysis. (DOCX)

Topological annotation of polymorphisms and disease associated mutations. Human protein variation data was downloaded from the UniProt database release 29-Oct-2014. The topology information was obtained from the HTP database version 1.0. The creation of this file is described in the Materials and Methods section of this paper. The abbreviations for...

Phenotypic variance and minor allele frequency of the glycine to arginine polymorphisms within the UniProt database. Glycine to arginine changes annotated as polymorphisms in the UniProt database. The table contains the gene name, the UniProt accession of the protein, the UniProt variant identifier, the rsID of the polymorphism (if applicable), phe...

The implementation of targeted therapies revolutionized oncology. As the number of new oncogenic driver mutations, which provide molecular targets for prediction of effective and selective therapies, is increasing, the implementation of fast and reliable methods by molecular pathology labs is very important. Here we report our results with TruSeq C...

The draft genome sequence of a novel Mycoplasma strain, designated Mycoplasma sp. HU2014, has been determined. The genome comprises 1,084,927 nucleotides and was obtained from a mycoplasma-infected culture of chicken DT40 cells. Phylogenetic analysis places this taxon in a group comprising the closely related species Mycoplasma yeatsii and Mycoplas...

The chicken DT40 cell line is a widely used model system in the study of multiple cellular processes due to the efficiency of homologous gene targeting. The cell line was derived from a bursal lymphoma induced by avian leukosis virus infection. In this study we characterized the genome of the cell line using whole genome shotgun sequencing and sing...

Background Mangalicas are fatty type local/rare pig breeds with an increasing presence in the niche pork market in Hungary and in other countries. To explore their genetic resources, we have analysed data from next-generation sequencing of an individual male from each of three Mangalica breeds along with a local male Duroc pig. Structural variation...

The genetic relationship between 195 Mangalica and 79 non-Mangalica pigs was studied using mitochondrial D-loop SNP genotyping. Altogether, 35 polymorphic sites and 27 haplotypes were identified. Of the haplotypes, eight and 16 are Mangalica and non-Mangalica specific, respectively, while three contain both Mangalica and non-Mangalica individuals....

Understanding the molecular interactions that lead to the establishment of the major body axes during embryogenesis is one of the main goals of developmental biology. Although the past two decades have revolutionized our knowledge about the genetic basis of these patterning processes, the list of genes involved in axis formation is unlikely to be c...

In silico binding site analysis for candidate and randomly selected genes. (XLS)

Sequence of PCR primers used for the nested PCR reactions. (DOC)

Majority of the candidate genes are upregulated after MBT. Using a previously published dataset ([31] in Main Text), we tested whether the expression of our candidate genes is upregulated at MBT, as expected. Our results show that indeed, this is the case for all, except two genes: map2k6 and tmem68. The former showed a weak maternal expression, wh...

Genes with stochastic early expression. Genes belonging to this class show stochastic expression at the onset of the zygotic transcription. We could detect clusters of cells both in wild type and ich embryos that upregulated these particular genes, but no clear pattern emerged. For aplnrb (A–F) and isg15 (G–N), the expression pattern later became m...

Identification of candidate genes. Genes showing a significant (more than 1.5 fold in the case of DESeq) upregulation after normalization were considered for further analysis. Two complementary approaches, DESeq ([29] in the Main Text) (A) and Cufflinks ([30] in the Main Text) (B) packages were used to identify differentially regulated genes. Posit...

Extended genomic region analysis of validated genes. (A) For multi-exon genes, statistical analysis of the first introns for enrichment in putative TcfLef, XVent1 or Pou5f1 binding sites yielded negative results. (B) In the 4 kb downstream genomic regions, we could not detect significant differences between the random and validated gene-sets in the...

Mangalica breeds are indigenous to Hungary and their breeding history dates back to about 200--250 years ago. They are fat-type pigs and have a rare curly hair phenotype. The aim of our study was to establish the relationships between these unique breeds and other European breeds. Based on a core sequence of 382 bp present in 2713 mitochondrial D-l...

The whole genome of Mangalica animals has been screened on the Illumina porcine chip giving the possibility (1) to replace the previously applied ten microsatellite markers by nine SNP loci to classify the Blond, Swallow-Belly and Red Mangalica individuals into three different breed groups (P>0.95); (2) to propose 54 SNP loci for parentage testing...

Antlers of deer display the fastest and most robust bone development in the animal kingdom. Deposition of the minerals in the cartilage preceding ossification is a specific feature of the developing antler. We have cloned 28 genes which are upregulated in the cartilaginous section (called mineralized cartilage) of the developing ("velvet") antler o...