Searching journal content for articles similar to Locke et al. 6 (2): 155.

Displaying results 1-10 of 4962

For checked items

view abstracts
download to citation manager

Select this article
Research: Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei
- Gregor Jessberger,
- Csilla Várnai,
- Roman R. Stocsits,
- Wen Tang,
- Georg Stary,
- and Jan-Michael Peters
Genome Res. December 2023 33: 2094-2107; Published in Advance December 21, 2023, doi:10.1101/gr.277865.123
.... These processes are fundamental for inheritance but incompletely understood. We analyzed these processes in the frog Xenopus laevis, whose sperm can be assembled into functional pronuclei in egg extracts in vitro. In such extracts, cohesin extrudes DNA into loops, but in vivo cohesin only assembles topologically...
Select this article
Research: Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently
- Sophia David,
- Christophe Rusniok,
- Massimo Mentasti,
- Laura Gomez-Valero,
- Simon R. Harris,
- Pierre Lechat,
- John Lees,
- Christophe Ginevra,
- Philippe Glaser,
- Laurence Ma,
- Christiane Bouchier,
- Anthony Underwood,
- Sophie Jarraud,
- Timothy G. Harrison,
- Julian Parkhill,
- and Carmen Buchrieser
Genome Res. November 2016 26: 1555-1564; Published in Advance September 23, 2016, doi:10.1101/gr.209536.116
.... 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27: 578–579. Bowers JR, Kitchel B, Driebe EM,MacCannell DR, Roe C, Lemmer D, deMan T, Rasheed JK, Engelthaler DM, Keim P, et al. 2015. Genomic analysis of the emergence and rapid global dissemination of the clonal group 258 Klebsiella...
OPEN ACCESS ARTICLE
Select this article
Research: Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland
- Danesh Moradigaravand,
- Christine J. Boinett,
- Veronique Martin,
- Sharon J. Peacock,
- and Julian Parkhill
Genome Res. August 2016 26: 1101-1109; Published in Advance July 18, 2016, doi:10.1101/gr.205245.116
...Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland Danesh Moradigaravand 1 , Christine J. Boinett 1 , Veronique Martin 2 , Sharon J. Peacock 1 , 3 , 4 and Julian...
OPEN ACCESS ARTICLE
Select this article
Method: SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data
- Hamim Zafar,
- Nicholas Navin,
- Ken Chen,
- and Luay Nakhleh
Genome Res. November 2019 29: 1847-1859; Published in Advance October 18, 2019, doi:10.1101/gr.243121.118
...SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell sequencing data Hamim Zafar1,2, Nicholas Navin3, Ken Chen2 and Luay Nakhleh1 1Department of Computer Science, Rice University, Houston, Texas 77005, USA; 2Department of Bioinformatics...
Select this article
METHODS: Contigs Built with Fingerprints, Markers, and FPC V4.7
- Carol Soderlund,
- Sean Humphray,
- Andrew Dunham,
- and Lisa French
Genome Res. November 1, 2000 10: 1772-1787; Published in Advance November 8, 2000, doi:10.1101/gr.GR-1375R
..., Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom Abstract Contigs have been assembled, and over 2800 clones selected for sequencing for human chromosomes 9, 10 and 13. Using the FPC (FingerPrinted Contig) software, the contigs are assembled with markers and complete...
Select this article
Methods: Systematic Recovery and Analysis of Full-ORF Human cDNA Clones
- Ágnes Baross,
- Yaron S.N. Butterfield,
- Shaun M. Coughlin,
- Thomas Zeng,
- Malachi Griffith,
- Obi L. Griffith,
- Anca S. Petrescu,
- Duane E. Smailus,
- Jaswinder Khattra,
- Helen L. McDonald,
- Sheldon J. McKay,
- Michelle Moksa,
- Robert A. Holt,
- and Marco A. Marra
Genome Res. October 15, 2004 14: 2083-2092; doi:10.1101/gr.2473704
...by polymerase chain reaction (PCR) amplification of transcripts in 96-well plates using gene-specific primer pairs flanking the ORFs. Amplicons are cloned into a sequencing vector, and full-length sequences are obtained. Sequences are processed and assembled using Phred and Phrap , and analyzed using Consed...
Select this article
RESOURCE: Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis
- Eiichi Shoguchi,
- Takeshi Kawashima,
- Yutaka Satou,
- Makoto Hamaguchi,
- Tadasu Sin-I,
- Yuji Kohara,
- Nik Putnam,
- Daniel S. Rokhsar,
- and Nori Satoh
Genome Res. February 2006 16: 297-303; Published in Advance December 14, 2005, doi:10.1101/gr.4156606
...genomic sequence onto chromosomes (for selected BAC clones, see Supplemental Table S1). We selected 139 BAC clones to cover 100 of the largest scaffolds assembled in the Ciona draft (v. 1.0) (Scaffold_1 to Scaffold_100), and another set of 23 BAC clones was selected to increase the accuracy...
Select this article
RESOURCE: Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae
- Yanhui Hu,
- Andreas Rolfs,
- Bhupinder Bhullar,
- Tellamraju V. S. Murthy,
- Cong Zhu,
- Michael F. Berger,
- Anamaria A. Camargo,
- Fontina Kelley,
- Seamus McCarron,
- Daniel Jepson,
- Aaron Richardson,
- Jacob Raphael,
- Donna Moreira,
- Elena Taycher,
- Dongmei Zuo,
- Stephanie Mohr,
- Michael F. Kane,
- Janice Williamson,
- Andrew Simpson,
- Martha L. Bulyk,
- Edward Harlow,
- Gerald Marsischky,
- Richard D. Kolodner,
- and Joshua LaBaer
Genome Res. April 2007 17: 536-543; Published in Advance February 23, 2007, doi:10.1101/gr.6037607
...cloning procedure. DNA sequencing reveals high-fidelity capture of 87% of known and predicted yeast ORFs To provide a well-annotated collection, we sequenced the complete insert (including the 5′ and 3′ att B sequences), assembled sequence contigs, and compared the assemblies to corresponding reference...
Select this article
LETTER: High Throughput Fingerprint Analysis of Large-Insert Clones
- Marco A. Marra,
- Tamara A. Kucaba,
- Nicole L. Dietrich,
- Eric D. Green,
- Buddy Brownstein,
- Richard K. Wilson,
- Ken M. McDonald,
- LaDeana W. Hillier,
- John D. McPherson,
- and Robert H. Waterston
Genome Res. November 1, 1997 7: 1072-1084; doi:10.1101/gr.7.11.1072
...assembly was conducted using a tolerance of 3 (see Methods: Computer Analysis and Contig Construction) all 107 rDNA clones that had been identified manually were placed into a single contig by FPC. One additional clone (G31K19) was also identified and placed in this contig by FPC. Comparison of this clone’s...
Select this article
Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...-to-telomere scaffolds by twofold, reduce runtime by fourfold, and improve assembly correctness. On a panel of 19 human s, Verkko2 assembles an average of 39 of 46 complete chromosomes as scaffolds, with 21 of these assembled as gapless contigs. Together, these improvements enable telomere-to-telomere comparative...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Locke et al. 6 (2): 155.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: