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Method: Accurate sequencing of DNA motifs able to form alternative (non-B) structures
- Matthias H. Weissensteiner,
- Marzia A. Cremona,
- Wilfried M. Guiblet,
- Nicholas Stoler,
- Robert S. Harris,
- Monika Cechova,
- Kristin A. Eckert,
- Francesca Chiaromonte,
- Yi-Fei Huang,
- and Kateryna D. Makova
Genome Res. July 11, 2023 ; Published in Advance July 11, 2023, doi:10.1101/gr.277490.122
...that elevated sequencing errors at non-B DNA motifs should be considered in lowread-depth studies (single-cell, ancient DNA, and pooled-sample population sequencing) and in scoring rare variants. Combining technologies should maximize sequencing accuracy in future studies of non-B DNA. [Supplemental material...
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Resource: Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii
- The Anopheles gambiae 1000 Genomes Consortium
Genome Res. October 2020 30: 1533-1546; Published in Advance September 28, 2020, doi:10.1101/gr.262790.120
...on the nucleotide sequence. This in turn suggests that the nucleotide sequence may serve as an important target for factors that bind to DNA or pre-mRNA molecules and control differential splicing. However, this region is >1 kbp distant from the putative homologs of the regulatory factor binding sequences (dsx...
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Methods: A new approach to estimate parameters of speciation models with application to apes
- Celine Becquet and
- Molly Przeworski
Genome Res. October 2007 17: 1505-1519; Published in Advance August 21, 2007, doi:10.1101/gr.6409707
...to the most recent common ancestor for both populations based on mitochondrial DNA (mtDNA) and a small number of microsatellites and autosomal and X-linked loci are ∼1.5–2.5 Mya ( Zhi et al. 1996 ; Kaessmann et al. 2001 ; Zhang et al. 2001 ), but to our knowledge, there are no published estimates...
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Method: An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data
- Yi Wang,
- James Lu,
- Jin Yu,
- Richard A. Gibbs,
- and Fuli Yu
Genome Res. May 2013 23: 833-842; Published in Advance January 7, 2013, doi:10.1101/gr.146084.112
...is defined as the probability of a reference read. If sequencing was error free, the binomial probability would be equal to 1, 0.5, and 0 for v = rr; ra; aa; in practice, this parameter deviates from ideal values due to sequencing variability. To estimate the value of these parameters, we employ...
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LETTER: CpG dinucleotides and the mutation rate of non-CpG DNA
- Jean-Claude Walser,
- Loïc Ponger,
- and Anthony V. Furano
Genome Res. September 2008 18: 1403-1414; Published in Advance June 11, 2008, doi:10.1101/gr.076455.108
...for comparing the extent of nucleotide differences (divergence) between neutrally evolving orthologous (syntenic) sequences in the species of interest. L1 retrotransposons reside in the host but can replicate autonomously by copying (retrotransposing) their RNA transcripts into genomic DNA. L1 copies...
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Research: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies
- PingHsun Hsieh,
- August E. Woerner,
- Jeffrey D. Wall,
- Joseph Lachance,
- Sarah A. Tishkoff,
- Ryan N. Gutenkunst,
- and Michael F. Hammer
Genome Res. March 2016 26: 291-300; Published in Advance February 17, 2016, doi:10.1101/gr.196634.115
...fossil bones and teeth have not been successful (Campana et al. 2013; Veeramah and Hammer 2014). Archaic introgression in Africa can thus not be studied by directly comparing DNA sequences from archaic and modern populations. Using a more indirect approach to infer archaic admixture, Plagnol and Wall...
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Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
...) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription...
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Research: In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors
- F.X. Reymond Sutandy,
- Stefanie Ebersberger,
- Lu Huang,
- Anke Busch,
- Maximilian Bach,
- Hyun-Seo Kang,
- Jörg Fallmann,
- Daniel Maticzka,
- Rolf Backofen,
- Peter F. Stadler,
- Kathi Zarnack,
- Michael Sattler,
- Stefan Legewie,
- and Julian König
Genome Res. May 2018 28: 699-713; Published in Advance April 11, 2018, doi:10.1101/gr.229757.117
...recognizes RNA sequences and how this is modulated by trans-acting RBPs. We measure U2AF2 affinities at hundreds of binding sites and compare in vitro and in vivo binding landscapes by mathematical modeling. We find that trans-acting RBPs extensively regulate U2AF2 binding in vivo, including enhanced...
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Research: Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species
- Eyal Elyashiv,
- Kevin Bullaughey,
- Shmuel Sattath,
- Yosef Rinott,
- Molly Przeworski,
- and Guy Sella
Genome Res. November 2010 20: 1558-1573; Published in Advance September 4, 2010, doi:10.1101/gr.108993.110
...) by assuming that the number of neutral mutations in a sample follows a Poisson distribution, the parameter of which depends on the sample size and u (Hudson 1990) and for nonsynonymous sites, on the sample size, u and f. For each pair of populations that we compared, we estimated the 12 parameters...
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Resource: GenGIS: A geospatial information system for genomic data
- Donovan H. Parks,
- Michael Porter,
- Sylvia Churcher,
- Suwen Wang,
- Christian Blouin,
- Jacqueline Whalley,
- Stephen Brooks,
- and Robert G. Beiko
Genome Res. October 2009 19: 1896-1904; Published in Advance July 27, 2009, doi:10.1101/gr.095612.109
...-community similarity, also known as beta-diversity. Since these sites have associated geographic points and habitat parameters, we can also consider the influence of site proximity on microbial community structure. We estimated the diversity at each site by retrieving all 16S rDNA sequences from each sample using...

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