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Method: HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
- Peter Edge,
- Vineet Bafna,
- and Vikas Bansal
Genome Res. May 2017 27: 801-812; Published in Advance December 9, 2016, doi:10.1101/gr.213462.116
...feasible with paired-end sequencing, i.e., pairs of short reads derived from the ends of long DNA fragments, but requires long and variable insert lengths to assemble long haplotypes (Tewhey et al. 2011). Selvaraj et al. (2013) used sequence data from a proximity ligation method (Hi-C) to assemble accurate...
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Method: A comprehensively molecular haplotype-resolved genome of a European individual
- Eun-Kyung Suk,
- Gayle K. McEwen,
- Jorge Duitama,
- Katja Nowick,
- Sabrina Schulz,
- Stefanie Palczewski,
- Stefan Schreiber,
- Dustin T. Holloway,
- Stephen McLaughlin,
- Heather Peckham,
- Clarence Lee,
- Thomas Huebsch,
- and Margret R. Hoehe
Genome Res. October 2011 21: 1672-1685; Published in Advance August 3, 2011, doi:10.1101/gr.125047.111
...sequencing (NGS) approach developed in direct continuation of our previously described fosmid pool-based molecular haplotyping approach (Burgtorf et al. 2003); a similar method was described recently (Kitzman et al. 2011). The completeness of our phasing allowed determination of the molecular haplotype pairs...
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Method: Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
- Nicholas H. Putnam,
- Brendan L. O'Connell,
- Jonathan C. Stites,
- Brandon J. Rice,
- Marco Blanchette,
- Robert Calef,
- Christopher J. Troll,
- Andrew Fields,
- Paul D. Hartley,
- Charles W. Sugnet,
- David Haussler,
- Daniel S. Rokhsar,
- and Richard E. Green
Genome Res. March 2016 26: 342-350; Published in Advance February 4, 2016, doi:10.1101/gr.193474.115
...generated (Shedlock et al. 2007) bacterial artificial chromosome (BAC) end sequences to the assembly. Of those, 1298 pairs were uniquely aligned by GMAP (Wu and Watanabe 2005) with 90% coverage and 95% identity to the assembly and the HiRise scaffolded version. In the input assembly, 12.5% of the BAC end...
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Resource: Detecting copy number variation with mated short reads
- Paul Medvedev,
- Marc Fiume,
- Misko Dzamba,
- Tim Smith,
- and Michael Brudno
Genome Res. November 2010 20: 1613-1622; Published in Advance August 30, 2010, doi:10.1101/gr.106344.110
...of the sequencing process (Dohm et al. 2008; Harismendy et al. 2009), whichmake it difficult to separate true changes in copy number from segments that are over- or undersampled by the sequencing technology. Alternatively, methods for SV detection have used clone-end sequencing data to detect variants (Raphael et...
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Resource: A high-resolution map of small-scale inversions in the gibbon genome
- Ludovica Mercuri,
- Donato Palmisano,
- Alberto L'Abbate,
- Pietro D'Addabbo,
- Francesco Montinaro,
- Claudia Rita Catacchio,
- Patrick Hasenfeld,
- Mario Ventura,
- Jan O. Korbel,
- Ashley D. Sanders,
- Flavia Angela Maria Maggiolini,
- and Francesca Antonacci
Genome Res. October 2022 32: 1941-1951; Published in Advance September 30, 2022, doi:10.1101/gr.276960.122
...sequence (BES) pair-mapping data from the same NLE individual used to generate the gibbon reference assembly. Because the BAC library belongs to an NLE and the Strand-seq was generated from an NSI, we expected some discrepancies for inversions that could be polymorphic between the two species. First...
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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
...because they have end pairs that are incorrectly oriented and map abnormally far apart when mapped to the human reference sequence. BES and fosmid-end sequence profiling of 372 BAC and 33 fosmid clones was used to study the orientation of 176 regions...
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Resource: Inversion variants in human and primate genomes
- Claudia Rita Catacchio,
- Flavia Angela Maria Maggiolini,
- Pietro D'Addabbo,
- Miriana Bitonto,
- Oronzo Capozzi,
- Martina Lepore Signorile,
- Mattia Miroballo,
- Nicoletta Archidiacono,
- Evan E. Eichler,
- Mario Ventura,
- and Francesca Antonacci
Genome Res. May 18, 2018 ; Published in Advance May 18, 2018, doi:10.1101/gr.234831.118
...of inversions came with the introduction of paired-end sequencing and mapping 4These authors contributed equally to this work. Corresponding author: francesca.antonacci@uniba.it Article published online before print. Article, supplemental material, and publication date are at http://www..org/cgi/doi/10.1101/gr...
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LETTER: A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome
- Oliver A. Hampton,
- Petra Den Hollander,
- Christopher A. Miller,
- David A. Delgado,
- Jian Li,
- Cristian Coarfa,
- Ronald A. Harris,
- Stephen Richards,
- Steven E. Scherer,
- Donna M. Muzny,
- Richard A. Gibbs,
- Adrian V. Lee,
- and Aleksandar Milosavljevic
Genome Res. February 2009 19: 167-177; Published in Advance December 3, 2008, doi:10.1101/gr.080259.108
..., as illustrated in Figure 1A . The bridging step utilizes end-sequence information from fosmid-sized clone inserts to connect chromosomal loci brought together at aberrant rearrangement-induced joins in the cancer . End-sequences of breakpoint-spanning fosmids were recognized as those that do not map onto...
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Research: Large duplications at reciprocal translocation breakpoints that might be the counterpart of large deletions and could arise from stalled replication bubbles
- Karen D. Howarth,
- Jessica C.M. Pole,
- Juliet C. Beavis,
- Elizabeth M. Batty,
- Scott Newman,
- Graham R. Bignell,
- and Paul A.W. Edwards
Genome Res. April 2011 21: 525-534; Published in Advance January 20, 2011, doi:10.1101/gr.114116.110
...products of the translocation, while the other daughter cell would show deletion. These duplications may have been overlooked because they may be missed by FISH and array-CGH and may be interpreted as insertions by paired-end sequencing. Such duplications may therefore be quite frequent. Footnotes...
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LETTER: Closing the Gaps on Human Chromosome 19 Revealed Genes With a High Density of Repetitive Tandemly Arrayed Elements
- Sun-Hee Leem,
- Natalay Kouprina,
- Jane Grimwood,
- Jung-Hyun Kim,
- Michael Mullokandov,
- Young-Ho Yoon,
- Ji-Youn Chae,
- Jenna Morgan,
- Susan Lucas,
- Paul Richardson,
- Chris Detter,
- Tijana Glavina,
- Eddy Rubin,
- J. Carl Barrett,
- and Vladimir Larionov
Genome Res. February 2004 14: 239-246; Published in Advance January 12, 2004, doi:10.1101/gr.1929904
...and UCSC (build 29, April, 2002) using BLAST. Positions of YAC ends for GAP1, GAP2, GAP3, and GAP6 TAR clones are shown in Table 1 . With knowledge of the size of the YACs, the positions of the YAC end sequences, and the hooks in the clones towards the gaps, we estimated their sizes: GAP1, ∼15 kb; GAP2...

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