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Variants of the Segment Number of a Graph [article]

Yoshio Okamoto, Alexander Ravsky, Alexander Wolff
2019 arXiv   pre-print
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]

Haishuai Wang
2017 arXiv   pre-print
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

Tuukka Norri, Bastien Cazaux, Saska Dönges, Daniel Valenzuela, Veli Mäkinen, Can Alkan
2021 Bioinformatics  
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]

Michael Sutton, Tal Ben-Nun, Amnon Barak, Sreepathi Pai, Keshav Pingali
2016 arXiv   pre-print
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

Adrien Leger, Ian Brettell, Jack Monahan, Carl Barton, Nadeshda Wolf, Natalja Kusminski, Cathrin Herder, Narendar Aadepu, Clara Becker, Jakob Gierten, Omar T. Hammouda, Eva Hasel (+14 others)
2022 Genome Biology  
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

Yeonghun Lee, Hyunju Lee
2021 Nature Communications  
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]

Maria Nattestad, Marley C. Alford, Fritz J. Sedlazeck, Michael C. Schatz
2016 bioRxiv   pre-print
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

Prof. Yuvaraju B N, Dr. Niranjan N Chiplunkar
2010 International Journal of Computer Applications  
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]

Adrien Leger, Ian Brettell, Jack Monahan, Carl Barton, Nadeshda Wolf, Natalja Kusminski, Cathrin Herder, Narendar Aadepu, Clara Becker, Jakob Gierten, Omar Hammouda, Eva Hasel (+12 others)
2021 bioRxiv   pre-print
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

Kevin McGuinness, Noel E. O'Connor
2013 2013 IEEE International Conference on Image Processing  
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

M-Hossein Moeinzadeh, Jun Yang, Evgeny Muzychenko, Giuseppe Gallone, David Heller, Knut Reinert, Stefan Haas, Martin Vingron, Alexander Schönhuth
2020 PLoS Computational Biology  
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

Fabio Galasso, Margret Keuper, Thomas Brox, Bernt Schiele
2014 2014 IEEE Conference on Computer Vision and Pattern Recognition  
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

Danang Crysnanto, Christine Wurmser, Hubert Pausch
2019 Genetics Selection Evolution  
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

Matthew Hayes, Jing Li
2015 BMC Genetics  
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

Chirag Jain, Neda Tavakoli, Srinivas Aluru
2021 Bioinformatics  
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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