Searching journal content for articles similar to Raices et al. 29 (7): 1115.

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  1. Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
    • Paul Ashford,
    • Alexander M. Frankell,
    • Zofia Piszka,
    • Camilla S.M. Pang,
    • Mahnaz Abbasian,
    • Maise Al Bakir,
    • Mariam Jamal-Hanjani,
    • Nicholas McGranahan,
    • Charles Swanton,
    • and Christine A. Orengo
    Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
    ...regions are susceptible to deleterious mutations in essential genes and the subsequent loss of these tumor cells under negative selection. Thus, duplication of haploid regions is thought to be one of the reasons for the high frequency (∼75% of tumors) of WGD in lung tumors (López et al. 2020; Dinh et al...
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  2. Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
    • Kai Otsuka,
    • Akihiko Sakashita,
    • So Maezawa,
    • Richard M. Schultz,
    • and Satoshi H. Namekawa
    Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
    ...; pachytene spermatocytes (PSs), which are in meiotic prophase I; and haploid round spermatids (RS) (Fig. 1C). We were able to classify the 363 murine protein-coding KZFPs into six major classes based on nonhierarchical k-means clustering analysis (Fig. 1B; Supplemental Table 1). Class I KZFPs include 85...
  3. Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
    • John Beaulaurier,
    • Lynn Ly,
    • J. Andrew Duty,
    • Carly Tyer,
    • Christian Stevens,
    • Chuan-Tien Hung,
    • Akash Sookdeo,
    • Alex W. Drong,
    • Shreyas Kowdle,
    • Axel Guzman-Solis,
    • Domenico Tortorella,
    • Daniel J. Turner,
    • Sissel Juul,
    • Scott Hickey,
    • and Benhur Lee
    Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
    ...-specific, haploid assembly was created using Flye and HapDup (Methods). Colored bars indicate the position on the contig of functional V, D, J, and C gene segments. (A) The fully phased IGH locus, with the dashed lines depicting alternative structures in sections where the assembly differs structurally between...
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  4. Research: Delayed DNA replication in haploid human embryonic stem cells
    • Matthew M. Edwards,
    • Michael V. Zuccaro,
    • Ido Sagi,
    • Qiliang Ding,
    • Dan Vershkov,
    • Nissim Benvenisty,
    • Dieter Egli,
    • and Amnon Koren
    Genome Res. December 2021 31: 2155-2169; Published in Advance November 22, 2021, doi:10.1101/gr.275953.121
    ...an approximately twofold higher expression of X-linked genes when compared to diploids (Sagi et al. 2016). Any of these differences, as well as the lack of homologous chromosomes per se, could underlie the instability of mammalian haploid cells.Diploidization resembles polyploidization, which also involves whole...
  5. Research: Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability
    • Richard J. Wang,
    • Gregg W.C. Thomas,
    • Muthuswamy Raveendran,
    • R. Alan Harris,
    • Harshavardhan Doddapaneni,
    • Donna M. Muzny,
    • John P. Capitanio,
    • Predrag Radivojac,
    • Jeffrey Rogers,
    • and Matthew W. Hahn
    Genome Res. June 2020 30: 826-834; Published in Advance May 27, 2020, doi:10.1101/gr.255174.119
    ...(x) is the callability of site x in that trio. We take x to be a site from the set of all haploid sites with depth between 20 and 60. This strategy assumes that the ability to correctly call each individual in the trio is independent, allowing us to estimate Ci(x) as where Cc, Cp, and Cm are the probability of calling...
  6. Research: Direct estimate of the rate of germline mutation in a bird
    • Linnéa Smeds,
    • Anna Qvarnström,
    • and Hans Ellegren
    Genome Res. September 2016 26: 1211-1218; Published in Advance July 13, 2016, doi:10.1101/gr.204669.116
    ...site per generation or per site per haploid . Based on a long-term field study of more than 1400 breeding attempts recorded during 20 yr, Brommer et al. (2004) reported the generation time of the (female) collared flycatcher to be 1.8 yr. This should be adjusted to 2.0 yr by taking differences...
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  7. Research: Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
    • Kyuha Choi,
    • Xiaohui Zhao,
    • Andrew J. Tock,
    • Christophe Lambing,
    • Charles J. Underwood,
    • Thomas J. Hardcastle,
    • Heïdi Serra,
    • Juhyun Kim,
    • Hyun Seob Cho,
    • Jaeil Kim,
    • Piotr A. Ziolkowski,
    • Nataliya E. Yelina,
    • Ildoo Hwang,
    • Robert A. Martienssen,
    • and Ian R. Henderson
    Genome Res. April 2018 28: 532-546; Published in Advance March 12, 2018, doi:10.1101/gr.225599.117
    .... Together, our work reveals a complex relationship between chromatin and meiotic DSBs within A. thaliana genes and transposons, with significance for the diversity and evolution of plant s.During meiosis, a single round of DNA replication is coupled to two rounds of chromosome segregation, producing haploid...
  8. Research: De novo rates and selection of large copy number variation
    • Andy Itsara,
    • Hao Wu,
    • Joshua D. Smith,
    • Deborah A. Nickerson,
    • Isabelle Romieu,
    • Stephanie J. London,
    • and Evan E. Eichler
    Genome Res. November 2010 20: 1469-1481; Published in Advance September 14, 2010, doi:10.1101/gr.107680.110
    ...of 772) per haploid per generation (m = 6.5 3 10#2;3 for CNVs >500 kb) (Fig. 2). This estimate is not significantly different from rates observed in control samples in previous studies with smaller sample sizes (Supplemental Table 7; Supplemental Fig. 8; Sebat et al. 2007; Xu et al. 2008). The de novo...
  9. Perspective: Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression
    • Lesley T. MacNeil and
    • Albertha J.M. Walhout
    Genome Res. May 2011 21: 645-657; Published in Advance February 4, 2011, doi:10.1101/gr.097378.109
    ...,’’ which is analogous to the notionof TF bindingmotifs that are overrepresented in TF target genes (Milo et al. 2002). Because they occur frequently, network motifs likely represent circuits that have provided selective advantages in evolution. Below, we discuss how network topologies and circuits can...
  10. LETTER: Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline
    • Laurent Duret,
    • Jean Cohen,
    • Claire Jubin,
    • Philippe Dessen,
    • Jean-François Goût,
    • Sylvain Mousset,
    • Jean-Marc Aury,
    • Olivier Jaillon,
    • Benjamin Noël,
    • Olivier Arnaiz,
    • Mireille Bétermier,
    • Patrick Wincker,
    • Eric Meyer,
    • and Linda Sperling
    Genome Res. April 2008 18: 585-596; Published in Advance February 6, 2008, doi:10.1101/gr.074534.107
    ..., an auto-fertilization process (autogamy) occurs, illustrated here. Autogamy begins with meiosis of the two MIC to yield eight haploid products, seven of which degenerate. The eighth haploid gametic nucleus copies itself by mitosis and the two identical haploid nuclei fuse to from a completely homozygous...
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