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Variants of the Segment Number of a Graph
[article]
2019
arXiv
pre-print
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The segment number of a planar graph is the smallest number of line segments whose union represents a crossing-free straight-line drawing of the given graph in the plane. ...
We first construct an infinite family of planar graphs where the classical segment number is asymptotically twice as large as each of the new variants of the segment number. ...
We thank the organizers and participants of the 2019 Dagstuhl seminar "Beyond-planar graphs: Combinatorics, Models and Algorithms". ...
arXiv:1908.08871v2
fatcat:twxnsaysa5dorfpkey25ejy2dy
Time-Variant Graph Classification
[article]
2017
arXiv
pre-print
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These changes in graph structure with respect to the temporal order present a new representation of the graph, in which an object corresponds to a set of time-variant graphs. ...
In this paper, we formulate a novel time-variant graph classification task and propose a new graph feature, called a graph-shapelet pattern, for learning and classifying time-variant graphs. ...
We obtain a set of weekly time-variant graph data, i.e., G, and the total number of weeks (number of sequences) is 40. ...
arXiv:1609.04350v2
fatcat:54hsghecwjhajbgtwmoskftbt4
Founder Reconstruction Enables Scalable and Seamless Pangenomic Analysis
2021
Bioinformatics
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Our implemented workflow uses GATK or BCFtools for variant calling, but the various steps of our workflow (e.g. vcf2multialign tool, founder reconstruction) can be of independent interest as a basis for ...
Results We present PanVC with founder sequences, a scalable and accurate variant calling workflow based on a multiple alignment of reference sequences. ...
For processing the data in the experiments, we used a variety of tools including GNU Parallel (Tange, 2011) and Snakemake (Mölder et al., 2021) . ...
doi:10.1093/bioinformatics/btab516
pmid:34260702
pmcid:PMC8665761
fatcat:pzrqvjvg3rf27lbqnhenkered4
Adaptive Work-Efficient Connected Components on the GPU
[article]
2016
arXiv
pre-print
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The results show a considerable increase in performance (up to 6.8×) over current state-of-the-art solutions. ...
This report presents an adaptive work-efficient approach for implementing the Connected Components algorithm on GPUs. ...
ACKNOWLEDGMENT This research was supported by the German Research Foundation (DFG) Priority Program 1648 "Software for exascale Computing" (SPP-EXA), research project FFMK; NSF grants 1218568, 1337281, ...
arXiv:1612.01178v1
fatcat:57gunbl3wnhdfimatvkip2ue64
Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
2022
Genome Biology
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Nanopore sequencing allows us to identify a large variety of high-quality structural variants, and we present results and methods using a pan-genome graph representation of 12 individual medaka lines. ...
We use Oxford Nanopore Technologies (ONT) long read data to further investigate the genomic and epigenomic landscapes of a subset of the MIKK panel. ...
Acknowledgements The authors acknowledge Thomas Seitz, and Irina Oks and Marzena Majewski for supporting the fish husbandry, and Alicia Günthel, Rachel Müller, and Beate Wittbrodt for laboratory assistance ...
doi:10.1186/s13059-022-02602-4
pmid:35189951
pmcid:PMC8862245
fatcat:d5qklpxdlza6vkapbdjt7jsare
Integrative reconstruction of cancer genome karyotypes using InfoGenomeR
2021
Nature Communications
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Using whole-genome sequencing data sets of patients with breast cancer, glioblastoma multiforme, and ovarian cancer, we demonstrate the analytical potential of InfoGenomeR. ...
Here, we present Integrative Framework for Genome Reconstruction (InfoGenomeR)-a graph-based framework that can reconstruct individual SVs into karyotypes based on whole-genome sequencing data, by integrating ...
The WGS data of lung cancer cell lines, TCGA samples, and metastatic breast cancer included pre-processed data (BAM) mapped to GRCh37, and variants were called in the same way as the paired-end HeLa and ...
doi:10.1038/s41467-021-22671-6
pmid:33927198
fatcat:gq3ioryg4zb7bfgsvfltlbzlii
SplitThreader: Exploration and analysis of rearrangements in cancer genomes
[article]
2016
bioRxiv
pre-print
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It also provides explanations when multiple variants affect the copy number state and obscure the contribution of a single variant, such as a deletion within a region that is overall amplified. ...
SplitThreader constructs a sequence graph of genomic rearrangements in the sample and uses a priority queue breadth-first search algorithm on the graph to search for novel interactions. ...
Variants are shown as connecting lines between the copy number profiles, and variants in the fusion path are shown as thicker black lines. The copy number profiles shown are segmented. ...
doi:10.1101/087981
fatcat:vwjdnrephbhaxpcrdshjxj45uu
Scenario Based Performance Analysis of variants of TCP using NS2-Simulator
2010
International Journal of Computer Applications
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have led to the need for a better understanding of fundamental issues in TCP optimization in MANETS.TCP primarily designed for wired networks, faces performance degradation when applied to the ad-hoc ...
Earlier work in MANETs focused on comparing the performance of different routing protocols. Our analysis is on performance of the variants of TCP in MANETS. ...
ACKNOWLEDGMENT The authors would like to thank Mr. Mohit T and Ms Manasa for their contribution to the programming for some associated experiments. They would also like to thank Dr. ...
doi:10.5120/855-1197
fatcat:hrxm5nbnurdyljcb3iz7rrdjcm
Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
[article]
2021
bioRxiv
pre-print
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We also present results and methods using a pan-genome graph representation of 12 individual medaka lines from the MIKK panel. ...
Nanopore sequencing allowed us to identify a much greater variety of high-quality structural variants compared with Illumina sequencing. ...
Acknowledgements The authors acknowledge Thomas Seitz, and Irina Oks and Marzena Majewski for supporting the fish husbandry, and Alicia Günthel, Rachel Müller and Beate Wittbrodt for laboratory assistance ...
doi:10.1101/2021.05.17.444424
fatcat:4poy6mypsbdirk6odjb2gecgqi
Improved graph cut segmentation by learning a contrast model on the fly
2013
2013 IEEE International Conference on Image Processing
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We compare our approach to the standard graph cuts algorithm and show that the contrast model allows a user to achieve a more accurate segmentation with fewer interactions. ...
This paper describes an extension to the graph cut interactive image segmentation algorithm based on a novel approach to addressing the well known small cut problem. ...
With this number of superpixels, the contrast based algorithm can update the segmentation given a new set of user interactions in approximately 370 ms on a standard desktop PC, which allows for a smooth ...
doi:10.1109/icip.2013.6738561
dblp:conf/icip/McGuinnessO13
fatcat:d2f4xlz3pvgm7jw7nwyoepsu4e
Ranbow: A fast and accurate method for polyploid haplotype reconstruction
2020
PLoS Computational Biology
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Haplotype reconstruction becomes more difficult for higher numbers of homologous chromosomes, as it is often the case for polyploid plants. ...
This complexity is compounded further by higher heterozygosity, which denotes the frequent presence of variants between haplotypes. ...
In addition, Ranbow constructs a multipartite graph where the nodes are haplotype segments reconstructed from read clusters. The number of haplotype segments is limited by the ploidy of the organism. ...
doi:10.1371/journal.pcbi.1007843
pmid:32469863
fatcat:n67u2cat5ncr5fj55a34fi5u7a
Spectral Graph Reduction for Efficient Image and Streaming Video Segmentation
2014
2014 IEEE Conference on Computer Vision and Pattern Recognition
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In this paper, we propose the use of a reduced graph based on superpixels. ...
In contrast to previous work, the reduced graph is reweighted such that the resulting segmentation is equivalent, under certain assumptions, to that of the full graph. ...
Acknowledgements We acknowledge partial funding by the ERC Starting Grant VideoLearn. ...
doi:10.1109/cvpr.2014.14
dblp:conf/cvpr/GalassoKBS14
fatcat:5xaamc4nn5be5ojticxgdtshdy
Accurate sequence variant genotyping in cattle using variation-aware genome graphs
2019
Genetics Selection Evolution
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Graph-based methods facilitate the comparison of sequencing reads to a variation-aware genome graph, which incorporates a collection of non-redundant DNA sequences that segregate within a species. ...
Genotyping of sequence variants typically involves, as a first step, the alignment of sequencing reads to a linear reference genome. ...
Sequencing of the Original Braunvieh bulls was partially funded from the Federal Office for Agriculture (FOAG), Bern, Switzerland. ...
doi:10.1186/s12711-019-0462-x
fatcat:fyfm3dfk2nedhee44gilmsaexa
An integrative framework for the identification of double minute chromosomes using next generation sequencing data
2015
BMC Genetics
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This information is used by a graph-based algorithm to predict the presence of double minute chromosomes. ...
Results: Using a previously published copy number variant algorithm and two structural variation prediction algorithms, we implemented our framework and tested it on a dataset consisting of simulated double ...
The full contents of the supplement are available online at http://www.biomedcentral.com/ bmcgenet/supplements/16/S2. ...
doi:10.1186/1471-2156-16-s2-s1
pmid:25953282
pmcid:PMC4423570
fatcat:m7aux324nbactjgyff2bqdiwdi
A variant selection framework for genome graphs
2021
Bioinformatics
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number of positions at which variants are listed or to minimize the total number of variants listed. ...
This framework leads to a rich set of problems based on the types of variants [e.g. single nucleotide polymorphisms (SNPs), indels or structural variants (SVs)], and whether the goal is to minimize the ...
Conflict of Interest: none declared. ...
doi:10.1093/bioinformatics/btab302
pmid:34252945
fatcat:uwnm72ctdrc7vo4esvrgwy7mcm
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