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PycoMeth: A toolbox for differential methylation testing from Nanopore methylation calls [article]

Rene H Snajder, Oliver Stegle, Marc Jan Bonder
2022 bioRxiv   pre-print
/pycometh • meth5: https://github.com/snajder-r/MetH5Format Benchmark scripts: https://github.com/snajder-r/benchmark_meth5 Figure 1 : 1 Figure 1: MetH5 file format.  ...  based on a single call were removed, since these obtained false significance from grouped Nanopolish calls being duplicated in the pseudo-bulk generation (Figure S1 ) • PycoMeth: https://github.com/snajder-r  ... 
doi:10.1101/2022.02.16.480699 fatcat:iwyhnc7nyjab3a5ahsgqtqfvzq

High-Throughput Characterization and Comparison of Microbial Communities

Bettina Halwachs, Johann Höftberger, Gernot Stocker, Rene Snajder, Gregor Gorkiewicz, Gerhard G. Thallinger
2013 Biomedical Engineering  
The analysis of the huge amount of generated sequence data as well as pyrosequencing noise and chimeric sequences originating from PCR amplification pose a considerable challenge to the individual researcher in doing microbiome studies. The unbiased knowledge about microbial community composition and -structure as well as the interactions with the human host microbiome can give important insights into its role in human health and disease. Here we introduce SnoWMAn, the high-throughput
more » ... analysis pipeline and additionally investigate the effects of sequencing noise on non denoised and data denoised using two different approaches.
doi:10.1515/bmt-2013-4312 pmid:24042957 fatcat:prctc4hoa5h5xcmcehpiqi5djy

QPCR: Application for real-time PCR data management and analysis

Stephan Pabinger, Gerhard G Thallinger, René Snajder, Heiko Eichhorn, Robert Rader, Zlatko Trajanoski
2009 BMC Bioinformatics  
Since its introduction quantitative real-time polymerase chain reaction (qPCR) has become the standard method for quantification of gene expression. Its high sensitivity, large dynamic range, and accuracy led to the development of numerous applications with an increasing number of samples to be analyzed. Data analysis consists of a number of steps, which have to be carried out in several different applications. Currently, no single tool is available which incorporates storage, management, and
more » ... ltiple methods covering the complete analysis pipeline. Results: QPCR is a versatile web-based Java application that allows to store, manage, and analyze data from relative quantification qPCR experiments. It comprises a parser to import generated data from qPCR instruments and includes a variety of analysis methods to calculate cycle-threshold and amplification efficiency values. The analysis pipeline includes technical and biological replicate handling, incorporation of sample or gene specific efficiency, normalization using single or multiple reference genes, inter-run calibration, and fold change calculation. Moreover, the application supports assessment of error propagation throughout all analysis steps and allows conducting statistical tests on biological replicates. Results can be visualized in customizable charts and exported for further investigation. Conclusion: We have developed a web-based system designed to enhance and facilitate the analysis of qPCR experiments. It covers the complete analysis workflow combining parsing, analysis, and generation of charts into one single application. The system is freely available at http:// genome.tugraz.at/QPCR
doi:10.1186/1471-2105-10-268 pmid:19712446 pmcid:PMC2741456 fatcat:fonten77vrcz7myjv4c4byffpe

GPViz: dynamic visualization of genomic regions and variants affecting protein domains

Rene Snajder, Zlatko Trajanoski, Hubert Hackl
2013 Computer applications in the biosciences : CABIOS  
GPViz is a versatile Java-based software for dynamic gene-centered visualization of genomic regions and/or variants. User-defined data can be loaded in common formats as resulting from analysis workflows used in sequencing applications and studied in the context of the gene, the corresponding transcript isoforms, proteins and their domains or other protein features. Both the genomic regions and variants can be also defined interactively. Various gene filter options are provided to enable an
more » ... rsection of variants, genomic regions and affected protein features. Finally, by using GPViz, we identified differentially expressed exons, which could indicate alternative splicing events, and found somatic variants in different cancer types affecting metabolic proteins. GPViz is freely available at http:// icbi.at/gpviz (released under GNU general public license), is based on Java 7 and can be used as a stand-alone or Web Start application.
doi:10.1093/bioinformatics/btt354 pmid:23782613 fatcat:rvqe5puldrh3vkkeyccuthjcxe

A robust ex vivo system to study cellular dynamics underlying mouse peri-implantation development [article]

Takafumi Ichikawa, Hui Ting Zhang, Laura Panavaite, Anna Erzberger, Dimitri Fabrèges, Rene Snajder, Adrian Wolny, Ekaterina Korotkevich, Nobuko Tsuchida Straeten, Lars Hufnagel, Anna Kreshuk, Takashi Hiiragi
2021 bioRxiv   pre-print
Upon implantation, mammalian embryos undergo major morphogenesis and key developmental processes such as body axis specification and gastrulation. However, limited accessibility obscures study of these crucial processes. Here, we develop an ex vivo Matrigel-collagen-based culture to recapitulate mouse development from E4.5 to 6.0. Our system not only recapitulates embryonic growth, axis initiation, and overall 3D architecture in 49% of cases, its compatibility with light-sheet microscopy
more » ... study of cellular dynamics through automatic cell segmentation. We find that upon implantation, release of the increasing tension in the polar trophectoderm is necessary for its constriction and invagination. The resulting extra-embryonic ectoderm plays a key role in growth, morphogenesis and patterning of the neighboring epiblast, which subsequently gives rise to all embryonic tissues. This 3D-ex vivo system thus offers an unprecedented access to peri-implantation development for in toto monitoring, measurement and spatio-temporally controlled perturbation, revealing a mechano-chemical interplay between extra-embryonic and embryonic tissues.
doi:10.1101/2021.08.22.457265 fatcat:kcis7fvsnfb43eomy3xflnhofm

SIMPLEX: Cloud-Enabled Pipeline for the Comprehensive Analysis of Exome Sequencing Data

Maria Fischer, Rene Snajder, Stephan Pabinger, Andreas Dander, Anna Schossig, Johannes Zschocke, Zlatko Trajanoski, Gernot Stocker, Gajendra P. S. Raghava
2012 PLoS ONE  
In recent studies, exome sequencing has proven to be a successful screening tool for the identification of candidate genes causing rare genetic diseases. Although underlying targeted sequencing methods are well established, necessary data handling and focused, structured analysis still remain demanding tasks. Here, we present a cloud-enabled autonomous analysis pipeline, which comprises the complete exome analysis workflow. The pipeline combines several in-house developed and published
more » ... ons to perform the following steps: (a) initial quality control, (b) intelligent data filtering and pre-processing, (c) sequence alignment to a reference genome, (d) SNP and DIP detection, (e) functional annotation of variants using different approaches, and (f) detailed report generation during various stages of the workflow. The pipeline connects the selected analysis steps, exposes all available parameters for customized usage, performs required data handling, and distributes computationally expensive tasks either on a dedicated high-performance computing infrastructure or on the Amazon cloud environment (EC2). The presented application has already been used in several research projects including studies to elucidate the role of rare genetic diseases. The pipeline is continuously tested and is publicly available under the GPL as a VirtualBox or Cloud image at http://simplex.i-med.ac.at; additional supplementary data is provided at http://www.icbi.at/exome.
doi:10.1371/journal.pone.0041948 pmid:22870267 pmcid:PMC3411592 fatcat:3kr7xvxdx5gcvkz3rjueqm5zmq

Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures [article]

Tobias Rausch, Rene Snajder, Adrien Leger, Milena Simovic, Oliver Stegle, Ewan Birney, Marc Jan Bonder, Aurelie Ernst, Jan O. Korbel
2022 bioRxiv   pre-print
Cancer genomes harbor a broad spectrum of structural variants (SV) driving tumorigenesis, a relevant subset of which are likely to escape discovery in short reads. We employed Oxford Nanopore Technologies (ONT) sequencing in a paired diagnostic and post-therapy medulloblastoma to unravel the haplotype-resolved somatic genetic and epigenetic landscape. We assemble complex rearrangements and such associated with telomeric sequences, including a 1.55 Megabasepair chromothripsis event. We uncover a
more » ... complex SV pattern termed "templated insertion thread", characterized by short (mostly <1kb) insertions showing prevalent self-concatenation into highly amplified structures of up to 50kbp in size. Templated insertion threads occur in 3% of cancers, with a prevalence ranging to 74% in liposarcoma, and frequent colocalization with chromothripsis. We also perform long-read based methylome profiling and discover allele-specific methylation (ASM) effects, complex rearrangements exhibiting differential methylation, and differential promoter methylation in seven cancer-driver genes. Our study shows the potential of long-read sequencing in cancer.
doi:10.1101/2022.02.20.480758 fatcat:nok5elj5pbgizmal3hgqjeqt4i

An ex vivo system to study cellular dynamics underlying mouse peri-implantation development

Takafumi Ichikawa, Hui Ting Zhang, Laura Panavaite, Anna Erzberger, Dimitri Fabrèges, Rene Snajder, Adrian Wolny, Ekaterina Korotkevich, Nobuko Tsuchida-Straeten, Lars Hufnagel, Anna Kreshuk, Takashi Hiiragi
2022 Developmental Cell  
Upon implantation, mammalian embryos undergo major morphogenesis and key developmental processes such as body axis specification and gastrulation. However, limited accessibility obscures the study of these crucial processes. Here, we develop an ex vivo Matrigel-collagen-based culture to recapitulate mouse development from E4.5 to E6.0. Our system not only recapitulates embryonic growth, axis initiation, and overall 3D architecture in 49% of the cases, but its compatibility with light-sheet
more » ... scopy also enables the study of cellular dynamics through automatic cell segmentation. We find that, upon implantation, release of the increasing tension in the polar trophectoderm is necessary for its constriction and invagination. The resulting extra-embryonic ectoderm plays a key role in growth, morphogenesis, and patterning of the neighboring epiblast, which subsequently gives rise to all embryonic tissues. This 3D ex vivo system thus offers unprecedented access to peri-implantation development for in toto monitoring, measurement, and spatiotemporally controlled perturbation, revealing a mechano-chemical interplay between extra-embryonic and embryonic tissues.
doi:10.1016/j.devcel.2021.12.023 pmid:35063082 pmcid:PMC8826647 fatcat:flpnxtrwuff3velomr2soe36nu

MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data

Stephan Pabinger, Rene Snajder, Timo Hardiman, Michaela Willi, Andreas Dander, Zlatko Trajanoski
2014 Database: The Journal of Biological Databases and Curation  
., Snajder,R., Hardiman,T. et al. MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data.  ... 
doi:10.1093/database/bau004 pmid:24532766 pmcid:PMC3924767 fatcat:xuqndi4r5fhufbs4acx3b54qd4

Functional Categories Associated with Clusters of Genes That Are Co-Expressed across the NCI-60 Cancer Cell Lines

Barry R. Zeeberg, William Reinhold, René Snajder, Gerhard G. Thallinger, John N. Weinstein, Kurt W. Kohn, Yves Pommier, Ilya Ulasov
2012 PLoS ONE  
The NCI-60 is a panel of 60 diverse human cancer cell lines used by the U.S. National Cancer Institute to screen compounds for anticancer activity. In the current study, gene expression levels from five platforms were integrated to yield a single composite transcriptome profile. The comprehensive and reliable nature of that dataset allows us to study gene coexpression across cancer cell lines. Methodology/Principal Findings: Hierarchical clustering revealed numerous clusters of genes in which
more » ... e genes co-vary across the NCI-60. To determine functional categorization associated with each cluster, we used the Gene Ontology (GO) Consortium database and the GoMiner tool. GO maps genes to hierarchically-organized biological process categories. GoMiner can leverage GO to perform ontological analyses of gene expression studies, generating a list of significant functional categories. Conclusions/Significance: GoMiner analysis revealed many clusters of coregulated genes that are associated with functional groupings of GO biological process categories. Notably, those categories arising from coherent co-expression groupings reflect cancer-related themes such as adhesion, cell migration, RNA splicing, immune response and signal transduction. Thus, these clusters demonstrate transcriptional coregulation of functionally-related genes.
doi:10.1371/journal.pone.0030317 pmid:22291933 pmcid:PMC3265467 fatcat:jtlqofxpq5d6zjzspdanw45pui

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy

Mihaela Angelova, Pornpimol Charoentong, Hubert Hackl, Maria L Fischer, Rene Snajder, Anne M Krogsdam, Maximilian J Waldner, Gabriela Bindea, Bernhard Mlecnik, Jerome Galon, Zlatko Trajanoski
2015 Genome Biology  
While large-scale cancer genomic projects are comprehensively characterizing the mutational spectrum of various cancers, so far little attention has been devoted to either define the antigenicity of these mutations or to characterize the immune responses they elicit. Here we present a strategy to characterize the immunophenotypes and the antigen-ome of human colorectal cancer. Results: We apply our strategy to a large colorectal cancer cohort (n = 598) and show that subpopulations of
more » ... trating lymphocytes are associated with distinct molecular phenotypes. The characterization of the antigenome shows that a large number of cancer-germline antigens are expressed in all patients. In contrast, neo-antigens are rarely shared between patients, indicating that cancer vaccination requires individualized strategy. Analysis of the genetic basis of the tumors reveals distinct tumor escape mechanisms for the patient subgroups. Hypermutated tumors are depleted of immunosuppressive cells and show upregulation of immunoinhibitory molecules. Non-hypermutated tumors are enriched with immunosuppressive cells, and the expression of immunoinhibitors and MHC molecules is downregulated. Reconstruction of the interaction network of tumor-infiltrating lymphocytes and immunomodulatory molecules followed by a validation with 11 independent cohorts (n = 1,945) identifies BCMA as a novel druggable target. Finally, linear regression modeling identifies major determinants of tumor immunogenicity, which include well-characterized modulators as well as a novel candidate, CCR8, which is then tested in an orthologous immunodeficient mouse model. Conclusions: The immunophenotypes of the tumors and the cancer antigenome remain widely unexplored, and our findings represent a step toward the development of personalized cancer immunotherapies.
doi:10.1186/s13059-015-0620-6 pmid:25853550 pmcid:PMC4377852 fatcat:gsuzxcbzhfcpbiwfgirsqwzlmu

SeqBench: Integrated solution for the management and analysis of exome sequencing data

Andreas Dander, Stephan Pabinger, Michael Sperk, Maria Fischer, Gernot Stocker, Zlatko Trajanoski
2014 BMC Research Notes  
Acknowledgements We would like to thank Rene Snajder and Mark Bessem for their contributions to this project.  ... 
doi:10.1186/1756-0500-7-43 pmid:24444368 pmcid:PMC3898724 fatcat:37ba43dd3fejfhbkt4uschkawa

NASLJEĐE METAFIZIČKOG KLUBA: PRAGMATIZAM ČARLSA SANDERSA PERSA

MILENA KARAPETROVIĆ
2020 ARHE  
Kako naglašava jedan od prvih američkih istoričara filozofije -Herbert Šnajder (Herbert W. Schneider): "Sve, otprilike, do 1820. bilo je 2 Č. S.  ...  E-mail adresa autorke: milena.karapetrovic@ff.unibl.org Šnajder, H., Istorija američke filosofije, Obod, Cetinje 1971., str. 101. Anderson, D.  ... 
doi:10.19090/arhe.2019.32.199-217 fatcat:epjirx3ouzgb7ankvpfe6wzoyq

Modeling of RF head exposure in children

J. Wiart, A. Hadjem, N. Gadi, I. Bloch, M.F. Wong, A. Pradier, D. Lautru, V.F. Hanna, C. Dale
2005 Bioelectromagnetics  
The authors gratefully acknowledge the advice of Dr René de Sèze from INERIS. REFERENCES READ PROOFS CAREFULLY • This will be your only chance to review these proofs.  ...  Patrick Snajder, Production Editor Phone: 201-748-8807 E-mail: psnajder@wiley.com Refer to journal acronym and article production number (i.e., BEM 00-001 for BioElectroMagnetics 00-001).  ... 
doi:10.1002/bem.20155 pmid:16142772 fatcat:4jdixvksgzblhkwpn64ikvrari

Contemporary sociology and the challenge of LGBT perspective

Marija Radoman
2016 Sociologija  
Tako je, povodom donošenja odluke Vrhovnog suda SAD-a da legalizuje istopolne brakove u celoj zemlji, predsednik Američke psihijatrijske asocijacije Rene Bajnder (Renée Binder) izjavio u ime te asocijacije  ...  Naime, oba autora, i Nidam i Šnajder, kritikuju teorijski formalizam u izučavanju srodstva i zauzimaju poziciju kulturnog relativizma, smatrajući da nisu moguće komparativne studije i razvijanje "opšteg  ... 
doi:10.2298/soc16s1324r fatcat:pjw3upvumzabhlos5jsks432pm
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