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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...the IGH locus remains incomplete. The high degree of polymorphism, repetitive sequences, copy number variations (CNVs), and SVs have posed significant challenges in characterizing the IGH locus on a large scale (Watson et al. 2015). As a result, IG genes have largely been excluded from -wide association...
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Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
- Sergey Koren,
- Zhigui Bao,
- Andrea Guarracino,
- Shujun Ou,
- Sara Goodwin,
- Katharine M. Jenike,
- Julian Lucas,
- Brandy McNulty,
- Jimin Park,
- Mikko Rautiainen,
- Arang Rhie,
- Dick Roelofs,
- Harrie Schneiders,
- Ilse Vrijenhoek,
- Koen Nijbroek,
- Olle Nordesjo,
- Sergey Nurk,
- Mike Vella,
- Katherine R. Lawrence,
- Doreen Ware,
- Michael C. Schatz,
- Erik Garrison,
- Sanwen Huang,
- William Richard McCombie,
- Karen H. Miga,
- Alexander H.J. Wittenberg,
- and Adam M. Phillippy
Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
...related to its nucleotide composition, and changes in this current over time are subsequently decoded through a basecalling algorithm. This process is challenged by noise in the electrical signal and different sequence contexts that share similar current profiles (Kovaka et al. 2024).Since the commercial...
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Method: Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
- Yuelin Liu,
- Xuan Cindy Li,
- Farid Rashidi Mehrabadi,
- Alejandro A. Schäffer,
- Drew Pratt,
- David R. Crawford,
- Salem Malikić,
- Erin K. Molloy,
- Vishaka Gopalan,
- Stephen M. Mount,
- Eytan Ruppin,
- Kenneth D. Aldape,
- and S. Cenk Sahinalp
Genome Res. July 2023 33: 1089-1100; Published in Advance June 14, 2023, doi:10.1101/gr.277608.122
...reasonable models, the optimal phylogeny from bulk sequencing data may not be unique. Therefore, recent efforts have looked beyond bulk sequencing data to elucidate the progression history of a tumor. In a major step toward this goal, Quinn et al. (2021) introduced technologies for cell lineage tracing...
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Method: SMASH, a fragmentation and sequencing method for genomic copy number analysis
- Zihua Wang,
- Peter Andrews,
- Jude Kendall,
- Beicong Ma,
- Inessa Hakker,
- Linda Rodgers,
- Michael Ronemus,
- Michael Wigler,
- and Dan Levy
Genome Res. June 2016 26: 844-851; Published in Advance April 14, 2016, doi:10.1101/gr.201491.115
.... If we exclude bases at the end of a read where fragments are typically too short to map, the 20:4 rule uses 85%–88% of bases sequenced (Supplemental Table S2). We employ the 20:4 rule throughout.Comparing WGS to SMASH profiles under optimized pipeline parametersWe compared the performance of WGS...
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Research: Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells
- Yan Gao,
- Xiaohui Ni,
- Hua Guo,
- Zhe Su,
- Yi Ba,
- Zhongsheng Tong,
- Zhi Guo,
- Xin Yao,
- Xixi Chen,
- Jian Yin,
- Zhao Yan,
- Lin Guo,
- Ying Liu,
- Fan Bai,
- X. Sunney Xie,
- and Ning Zhang
Genome Res. August 2017 27: 1312-1322; Published in Advance May 9, 2017, doi:10.1101/gr.216788.116
.... Cell 153: 666–677. Baslan T, Kendall J, Ward B, Cox H, Leotta A, Rodgers L, Riggs M, D’Italia S, Sun G, Yong M, et al. 2015. Optimizing sparse sequencing of single cells for highly multiplex copy number profiling. Genome Res 25: 714–724. Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, Linhart D...
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Method: Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns
- Alla Mikheenko,
- Andrey D. Prjibelski,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. April 2022 32: 726-737; Published in Advance March 17, 2022, doi:10.1101/gr.276405.121
...molecule. Here, we present a novel platform-comparison method that combines barcoding strategies and long-read sequencing to sequence cDNA copies representing an individual RNA molecule on both Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). We compare these long-read pairs in terms...
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Research: Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays
- Jeremiah H. Li,
- Chase A. Mazur,
- Tomaz Berisa,
- and Joseph K. Pickrell
Genome Res. April 2021 31: 529-537; Published in Advance February 3, 2021, doi:10.1101/gr.266486.120
...-pass sequencing can be achieved by multiplexing large numbers of samples to reduce cost, and (4) the fact that the average expected accuracy of a sample's imputed genotypes can be fine-tuned by adjusting the target coverage for the sample, something which is useful when designing experiments within real...
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Methods: Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
- Jin Billy Li,
- Yuan Gao,
- John Aach,
- Kun Zhang,
- Gregory V. Kryukov,
- Bin Xie,
- Annika Ahlford,
- Jung-Ki Yoon,
- Abraham M. Rosenbaum,
- Alexander Wait Zaranek,
- Emily LeProust,
- Shamil R. Sunyaev,
- and George M. Church
Genome Res. September 2009 19: 1606-1615; Published in Advance June 12, 2009, doi:10.1101/gr.092213.109
...Multiplex padlock targeted sequencing reveals human hypermutable CpG variations Jin Billy Li 1 , 6 , 9 , Yuan Gao 2 , 6 , John Aach 1 , 6 , Kun Zhang 3 , 6 , Gregory V. Kryukov 4 , 6 , Bin Xie 2 , Annika Ahlford 1...
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Research: Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer
- Marco L. Leung,
- Alexander Davis,
- Ruli Gao,
- Anna Casasent,
- Yong Wang,
- Emi Sei,
- Eduardo Vilar,
- Dipen Maru,
- Scott Kopetz,
- and Nicholas E. Navin
Genome Res. August 2017 27: 1287-1299; Published in Advance May 25, 2017, doi:10.1101/gr.209973.116
...intra-tumor heterogeneity at the primary and metastatic tumor sites. To address this problem, we developed a highly multiplexed single-cell DNA sequencing approach to trace the metastatic lineages of two CRC patients with matched liver metastases. Single-cell copy number or mutational profiling...
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Method: Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations
- Rachael J.M. Bashford-Rogers,
- Anne L. Palser,
- Brian J. Huntly,
- Richard Rance,
- George S. Vassiliou,
- George A. Follows,
- and Paul Kellam
Genome Res. November 2013 23: 1874-1884; Published in Advance June 6, 2013, doi:10.1101/gr.154815.113
...of BCRs (Dimitrov 2010; Benichou et al. 2012). There are several methods for isolation, amplification, and sequencing of B-cell repertoires. Multiplex PCR amplification, using degenerate PCR primers complementary to germ-line V and J segments have been designed and validated previously (vanDongen et al...
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