Searching journal content for articles similar to Veeramachaneni and Makałowski 14 (6): 1160.

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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...Pan analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility Dongying Xie1,2,3, Pohao Ye1,3, Yiming Ma1 and Zhongying Zhao1 1Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China; 2Institute for Research...
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Method: k-mer manifold approximation and projection for visualizing DNA sequences
- Chengbo Fu,
- Einari A. Niskanen,
- Gong-Hong Wei,
- Zhirong Yang,
- Marta Sanvicente-García,
- Marc Güell,
- and Lu Cheng
Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
...are pooled and sampled with the weights given by their counts. Random k-mers are sampled in a similar manner to reflect the background noise. A detailed description of the motif discovery algorithm is provided in Supplemental Note S2.We visualize the sampled k-mers X = (x1, x2, … , xN) by projecting them...
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Resource: Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform
- Liubomir Chorbadjiev,
- Murat Cokol,
- Zohar Weinstein,
- Kevin Shi,
- Christopher Fleisch,
- Nikolay Dimitrov,
- Svetlin Mladenov,
- Ivo Todorov,
- Iordan Ivanov,
- Simon Xu,
- Steven Ford,
- Yoon-ha Lee,
- Boris Yamrom,
- Steven Marks,
- Adriana Munoz,
- Alex Lash,
- Natalia Volfovsky,
- and Ivan Iossifov
Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
...York 11724, USA ↵7 These authors contributed equally to this work. Corresponding author: iossifov@cshl.eduAbstractThe exploration of genotypic variants impacting phenotypes is a cornerstone in genetics research. The emergence of vast collections containing deeply genotyped and phenotyped families has...
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Method: Protein domain embeddings for fast and accurate similarity search
- Benjamin Giovanni Iovino,
- Haixu Tang,
- and Yuzhen Ye
Genome Res. September 2024 34: 1434-1444; Published in Advance September 5, 2024, doi:10.1101/gr.279127.124
...against a target database to identify similar hits. This benchmark takes CATH v4.2.0 and clusters sequences more than 20% identical, resulting in 14,433 domain sequences across 5125 families. All domains were added to the target database, and 10,874 domains from 1566 of the families with more than one...
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Research: Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity
- Angela Jimeno-Martín,
- Erick Sousa,
- Rebeca Brocal-Ruiz,
- Noemi Daroqui,
- Miren Maicas,
- and Nuria Flames
Genome Res. March 2022 32: 459-473; Published in Advance January 24, 2022, doi:10.1101/gr.275623.121
.... We could not differentiate between RIC and RIM owing to proximity and morphological similarity; thus, they were scored as a unique category. (E) TF family distribution of TFs in C. elegans , TFs retrieved in our RNAi screen, TFs confirmed by mutant analysis, and mutant alleles with any assigned...
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Method: Identification of pathogenic variant enriched regions across genes and gene families
- Eduardo Pérez-Palma,
- Patrick May,
- Sumaiya Iqbal,
- Lisa-Marie Niestroj,
- Juanjiangmeng Du,
- Henrike O. Heyne,
- Jessica A. Castrillon,
- Anne O'Donnell-Luria,
- Peter Nürnberg,
- Aarno Palotie,
- Mark Daly,
- and Dennis Lal
Genome Res. January 2020 30: 62-71; Published in Advance December 23, 2019, doi:10.1101/gr.252601.119
...through “PER viewer,” a user-friendly online platform for interactive data mining, visualization, and download. In summary, our gene-family burden analysis approach identified novel PERs in protein sequences. This annotation can empower variant interpretation.Sequencing technologies are becoming routinely...
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Method: A pedigree-based prediction model identifies carriers of deleterious de novo mutations in families with Li-Fraumeni syndrome
- Fan Gao,
- Xuedong Pan,
- Elissa B. Dodd-Eaton,
- Carlos Vera Recio,
- Matthew D. Montierth,
- Jasmina Bojadzieva,
- Phuong L. Mai,
- Kristin Zelley,
- Valen E. Johnson,
- Danielle Braun,
- Kim E. Nichols,
- Judy E. Garber,
- Sharon A. Savage,
- Louise C. Strong,
- and Wenyi Wang
Genome Res. August 2020 30: 1170-1180; Published in Advance August 18, 2020, doi:10.1101/gr.249599.119
...carrier, and the probability of the mutation being de novo for the counselee is 0.0033. It is likely that this is a familial mutation inherited from the counselee's mother. Figure 1B shows a similar pedigree with three cancer patients, with one less affected relative in the maternal branch...
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Research: Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation
- Wesley A. Brashear,
- Terje Raudsepp,
- and William J. Murphy
Genome Res. December 2018 28: 1841-1851; Published in Advance October 31, 2018, doi:10.1101/gr.237586.118
...ampliconic sequence dispersed across the domestic cat Y Chromosome, and identified the major ampliconic gene families and repeat units. We analyzed fluorescence in situ hybridization, qPCR, and whole- sequence data from 20 cat species and revealed that ampliconic gene families are conserved across the cat...
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Research: Deep taxon sampling reveals the evolutionary dynamics of novel gene families in Pristionchus nematodes
- Neel Prabh,
- Waltraud Roeseler,
- Hanh Witte,
- Gabi Eberhardt,
- Ralf J. Sommer,
- and Christian Rödelsperger
Genome Res. November 2018 28: 1664-1674; Published in Advance September 19, 2018, doi:10.1101/gr.234971.118
...and sequenced six additional Pristionchus and two outgroup species. This resulted in 10 s with a ladder-like phylogeny, sequenced in one laboratory using the same platform and analyzed by the same bioinformatic procedures. Our analysis revealed that 68%–81% of genes are assignable to orthologous gene families...
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Research: A widespread role of the motif environment in transcription factor binding across diverse protein families
- Iris Dror,
- Tamar Golan,
- Carmit Levy,
- Remo Rohs,
- and Yael Mandel-Gutfreund
Genome Res. September 2015 25: 1268-1280; Published in Advance July 9, 2015, doi:10.1101/gr.184671.114
...high similarity to the corebinding motif. Notably, the regions around the binding sites of TFs that belong to the same TF families exhibited similar features, with high agreement between the in vitro and in vivo data sets. We propose that these unique features assist in guiding TFs to their cognate...
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