A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Filters
SENSITIVITY ANALYSIS FOR REVERSAL DISTANCE AND BREAKPOINT REUSE IN GENOME REARRANGEMENTS
2007
Biocomputing 2008
Preserved Fulltext
between genomes, namely the reversal distance and breakpoint reuse. ...
Breakpoint reuse is also strongly correlated with evolutionary distances, increasing for pairs of more divergent genomes. ...
Acknowledgements We would like to thank the reviewers for their insightful comments and suggestions. This work has been partially supported by NIH grant R01 AR050688. ...
doi:10.1142/9789812776136_0005
fatcat:buhvqef77fa2fm5djpf6suhae4
The rise and fall of breakpoint reuse depending on genome resolution
2011
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Some years ago, a controversy erupted in genome rearrangement studies over whether rearrangements recur, causing breakpoints to be reused. ...
Some years ago, a controversy erupted in genome rearrangement studies over whether rearrangements recur, causing breakpoints to be reused. ...
We thank Glenn Tesler for clarifying issues around internal vs external breakpoints as well as the differences in breakpoint reuse between the DCJ and HP formulations. ...
doi:10.1186/1471-2105-12-s9-s1
pmid:22151330
pmcid:PMC3283316
fatcat:2oa7yledbnh4xomejtih4w6wlu
SplitThreader: Exploration and analysis of rearrangements in cancer genomes
[article]
2016
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Here we present SplitThreader (http://splitthreader.com), an open- source interactive web application for analysis and visualization of genomic rearrangements and copy number variation in cancer genomes ...
This is applied to detect gene fusions and other novel sequences, as well as to evaluate distances in the rearranged genome between any genomic regions of interest, especially the repositioning of regulatory ...
If the end port is entered and the start port is exited, then this represents reading the sequence in the reverse complement All rights reserved. No reuse allowed without permission. ...
doi:10.1101/087981
fatcat:vwjdnrephbhaxpcrdshjxj45uu
Chromosomal Breakpoint Reuse in Genome Sequence Rearrangement
2005
Journal of Computational Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
In order to apply gene-order rearrangement algorithms to the comparison of genome sequences, Pevzner and Tesler bypass gene finding and ortholog identification and use the order of homologous blocks of ...
Analytic and simulation methods show that reuse is very sensitive to the proportion of blocks excluded. ...
D.S. holds the Canada Research Chair in Mathematical Genomics and is a Fellow in the Evolutionary Biology Program of the Canadian Institute for Advanced Research. ...
doi:10.1089/cmb.2005.12.812
pmid:16108718
fatcat:itu7y3uncvhkhb6ll5n76xnunu
Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss
2016
Journal of Computational Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
One of the key obstacles for MGRA and other similar tools is presence of breakpoint reuses when the same breakpoint region is broken by several different genome rearrangements in the course of evolution ...
Furthermore, MGRA2 employs a number of novel heuristics to cope with higher breakpoint reuse and process datasets inaccessible for MGRA. ...
to cope with higher breakpoint reuse and process datasets inaccessible for MGRA. ...
doi:10.1089/cmb.2015.0160
pmid:26885568
fatcat:hip5sakfhzfudankl2iazhxesy
Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny
2011
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Importantly, we show that this result holds for loci located on the same chromosome regardless of the genomic distance separating them, and the signal is stronger in gene-rich and open-chromatin regions ...
Results: In this paper, we analysed the correlation between two datasets: (i) whole-genome chromatin contact data obtained in human cells using the Hi-C protocol; and (ii) a set of breakpoint regions resulting ...
Acknowledgements The authors would like to thank Franck Picard for helpful discussions on the statistical analysis carried out in this article. This work was funded by the ...
doi:10.1186/1471-2164-12-303
pmid:21663614
pmcid:PMC3132170
fatcat:s2czlpbe5rghrhryygeg6tpdw4
Reconstruction of ancestral genomes in presence of gene gain and loss
[article]
2016
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
One of the key obstacles for MGRA and other similar tools is presence of breakpoint reuses when the same breakpoint region is broken by several different genome rearrangements in the course of evolution ...
Furthermore, MGRA2 employs a number of novel heuristics to cope with higher breakpoint reuse and process datasets inaccessible for MGRA. ...
to cope with higher breakpoint reuse and process datasets inaccessible for MGRA. ...
doi:10.1101/040196
fatcat:7mgw55xeefexbc2dhlsfkx3vde
Genome-wide detection of structural variants and indels by local assembly
[article]
2017
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
SvABA demonstrates superior sensitivity and specificity across a large spectrum of SVs, and substantially improved detection performance for variants in the 20-300 bp range, compared with existing methods ...
We applied SvABA to 344 cancer genomes from 11 cancer types, and found that templated-sequence insertions occur in ~4% of all somatic rearrangements. ...
Acknowledgements The National Institutes of Health (T32 HG002295/HG/ NHGRI, U54CA143798, and
Disclosure declaration The authors declare that there is no conflict of interest. ...
doi:10.1101/105080
fatcat:j5r4nxsbpzht5jjqgoeyywilmq
Microinversions in mammalian evolution
2006
Proceedings of the National Academy of Sciences of the United States of America
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
However, reverse-strand local alignments may also be caused by palindromes and inverted repeats (Fig. . ¶ We limited our analysis to genomes with no more than 200,000 unfinished base pairs. ...
We estimate that there exist hundreds of thousands of microinversions in genomes of mammals from comparative sequencing projects, an untapped source of new phylogenetic characters. genome rearrangements ...
We are grateful to Jian Ma and Jim Kent for the comparative analysis of humanchimpanzee microinversions found in this paper and many useful comments. ...
doi:10.1073/pnas.0603984103
pmid:17189424
pmcid:PMC1750909
fatcat:5ygns6oxuncmznhclf4gzb25by
Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions
2007
Genome Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Twenty-two of the 31 breakpoint regions have been reused repeatedly as rearrangement breakpoints in vertebrate evolution. ...
in GC content and CpG islands, highlighting a potential role for these features in genome instability. ...
Acknowledgments We thank Elbert Branscomb, Joomyeong Kim, and Alice Yamada for critical reviews of the manuscript, Gawain Lavers for website development, and the following individuals for their contribu-tions ...
doi:10.1101/gr.6775107
pmid:17921355
pmcid:PMC2045143
fatcat:sbo7uhsezfhvhhrnchtccozvdy
Long-range regulation is a major driving force in maintaining genome integrity
2009
BMC Evolutionary Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Large-scale genome rearrangement events modify the order of genes and non-coding conserved regions on chromosomes. ...
In many regions, the fitness cost of altering the spatial association between long-range regulatory regions and their target genes may be so high that rearrangements are not allowed. ...
We also wish to thank Francois Spitz from EMBL Heidelberg and Rob Sladek from McGill University for useful discussions. We also thank the reviewers for their helpful comments and suggestions. ...
doi:10.1186/1471-2148-9-203
pmid:19682388
pmcid:PMC2741452
fatcat:royggde6kjcullndfku46zoie4
Rearrangement Models and Single-Cut Operations
[chapter]
2009
Lecture Notes in Computer Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2013; you can also visit the original URL.
The file type is application/pdf.
There have been many widely used genome rearrangement models, such as reversals, Hannenhalli-Pevzner, and double-cut and join. ...
In this paper, we give a formal set-theoretic definition, which allows us to investigate and prove relationships between distances under various existing and new models. ...
Most of the work was done while PM was a member of the International NRW Graduate School in Bioinformatics and Genome Research, and the AG Genominformatik group at Bielefeld, while being additionally funded ...
doi:10.1007/978-3-642-04744-2_8
fatcat:v2negq2yjjespmwaifthtifmxq
Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers
[article]
2021
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Analysis of 105 HPV-positive oropharyngeal cancers by whole genome sequencing detects viral integration in 77%, revealing five statistically significant integration hotspots near genes that regulate epithelial ...
Human papillomavirus (HPV) causes 5% of all cancers and frequently integrates into host chromosomes, but the impacts of integration in tumorigenesis remain unclear. ...
(D) Comparison of gene counts (y-axis) expressed at various levels (Z-scores, x-axis), grouped in 50 kb genomic distances from the nearest breakpoint, in tumors with (red) and without (blue) breakpoints ...
doi:10.1101/2021.06.20.449168
fatcat:yjcax3scdvf5hczwsta7xsi5r4
Fine-mapping complex inversion breakpoints and investigating somatic pairing in the Anopheles gambiae species complex using proximity-ligation sequencing
[article]
2019
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
We found that inversion breakpoints occur in large repetitive regions, and strikingly among three inversions analyzed, two breakpoints appear to be reused in two separate inversions. ...
Here, we develop an approach that uses Hi-C sequencing data to molecularly fine-map the breakpoints of inversions 2Rbc and 2Rd in A. coluzzii. ...
Dotson, Principal Investigator for MR4 Vector Activity, for kindly supplying Mali-NIH, Pimperena, and Nkdokayo mosquitoes, and H. Ranson for sharing the Banfora M colony. ...
doi:10.1101/662114
fatcat:xdpes5j3pzgsxnnhukeqpim5wu
Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions
2018
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Motivation: Problems of genome rearrangement are central in both evolution and cancer research. ...
Most genome rearrangement models assume that the genome contains a single copy of each gene and the only changes in the genome are structural, i.e., reordering of segments. ...
Funding Study supported in part by the Bella Walter Memorial Fund of the Israel Cancer Association and by Len Blavatnik and the Blavatnik Family foundation. ...
doi:10.1093/bioinformatics/bty381
pmid:29726899
fatcat:6m6bmifjpvcqpns7gedilpbteu
« Previous
Showing results 1 — 15 out of 182 results