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Method: OMA standalone: orthology inference among public and custom genomes and transcriptomes
- Adrian M. Altenhoff,
- Jeremy Levy,
- Magdalena Zarowiecki,
- Bartłomiej Tomiczek,
- Alex Warwick Vesztrocy,
- Daniel A. Dalquen,
- Steven Müller,
- Maximilian J. Telford,
- Natasha M. Glover,
- David Dylus,
- and Christophe Dessimoz
Genome Res. July 2019 29: 1152-1163; Published in Advance June 24, 2019, doi:10.1101/gr.243212.118
...sets of genomic and transcriptomic protein predictions from Saccoglossus kowalevskii, Brachionus plicatilis, Adineta ricciae, Schmidtea mediterranea, Lumbricus rubellus, Chaetopleura apiculata, Sepia officinalis, Mytilus californianus, Biomphalaria glabrata, Lymnaea stagnalis, Hydra magnipapillata...
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Method: Efficient identification of Y chromosome sequences in the human and Drosophila genomes
- Antonio Bernardo Carvalho and
- Andrew G. Clark
Genome Res. November 2013 23: 1894-1907; Published in Advance August 6, 2013, doi:10.1101/gr.156034.113
...portion of chromosomes assemble into large and easily studied scaffolds, whereas heterochromatic regions are represented by thousands of small unmapped scaffolds (International Chicken Genome Sequencing Consortium 2004;Hoskins et al. 2007; Levy et al. 2007). Exons of heterochromatic genes and other...
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Method: Accurate and fast graph-based pangenome annotation and clustering with ggCaller
- Samuel T. Horsfield,
- Gerry Tonkin-Hill,
- Nicholas J. Croucher,
- and John A. Lees
Genome Res. September 2023 33: 1622-1637; Published in Advance August 24, 2023, doi:10.1101/gr.277733.123
...applied ggCaller to simulated and real-world bacterial data sets containing hundreds or thousands of s, comparing it to current state-of-the-art tools. ggCaller has considerable speed-ups with equivalent or greater accuracy, particularly with data sets containing complex sources of error, such as assembly...
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Methods: Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes
- Nitin Gupta,
- Jamal Benhamida,
- Vipul Bhargava,
- Daniel Goodman,
- Elisabeth Kain,
- Ian Kerman,
- Ngan Nguyen,
- Noah Ollikainen,
- Jesse Rodriguez,
- Jian Wang,
- Mary S. Lipton,
- Margaret Romine,
- Vineet Bafna,
- Richard D. Smith,
- and Pavel A. Pevzner
Genome Res. July 2008 18: 1133-1142; Published in Advance April 21, 2008, doi:10.1101/gr.074344.107
...). Such proteogenomic approaches further improve gene predictions and allow one to address problems that remained beyond the reach of both traditional gene prediction tools and comparative genomics. We recently developed MS-Genome software for automated proteogenomic annotation of bacterial s ( Gupta et al. 2007...
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Method: Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
- Byron J. Smith,
- Chunyu Zhao,
- Veronika Dubinkina,
- Xiaofan Jin,
- Liron Zahavi,
- Saar Shoer,
- Jacqueline Moltzau-Anderson,
- Eran Segal,
- and Katherine S. Pollard
Genome Res. May 2025 35: 1247-1260; Published in Advance April 10, 2025, doi:10.1101/gr.279543.124
...of Epidemiology and Biostatistics, University of California, San Francisco, California 94158, USA Corresponding author: katherine.pollard@gladstone.ucsf.eduAbstractMetagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity of bacterial species within and across...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...the Mendelian concordance rate among trios and eliminates tens of thousands of spurious SNVs per sample, including a reduction of false positives in 269 challenging, medically relevant genes by up to a factor of 12 (Aganezov et al. 2022). Altogether, the T2T consortium has opened previously inaccessible genomic...
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Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
- Nikolaos Vakirlis and
- Anne Kupczok
Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
...from annotation errors, because they are typically detected by comparative genomics approaches. These in turn rely on the automatic prediction of protein-coding open reading frames (ORFs) and sequence similarity searches between species, both potential sources of artifacts in the form of spurious ORFs...
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Research: Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome
- Daniela S. Aliaga Goltsman,
- Christine L. Sun,
- Diana M. Proctor,
- Daniel B. DiGiulio,
- Anna Robaczewska,
- Brian C. Thomas,
- Gary M. Shaw,
- David K. Stevenson,
- Susan P. Holmes,
- Jillian F. Banfield,
- and David A. Relman
Genome Res. October 2018 28: 1467-1480; Published in Advance September 19, 2018, doi:10.1101/gr.236000.118
...in the reconstructed s (from re-arrangements and genomic islands) and in the SNP patterns, we believe that the strains are not identical and are, therefore, likely not due to contamination. Colonization of the vagina and gut body sites is unlikely to occur independently (the same vaginal species was always found...
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Research: Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
- Stephen J. Salipante,
- David J. Roach,
- Jacob O. Kitzman,
- Matthew W. Snyder,
- Bethany Stackhouse,
- Susan M. Butler-Wu,
- Choli Lee,
- Brad T. Cookson,
- and Jay Shendure
Genome Res. January 2015 25: 119-128; Published in Advance November 4, 2014, doi:10.1101/gr.180190.114
..., is unknown, sharing of E. coli strains among close contacts is documented (Foxman et al. 1997; Johnson et al. 2008). Although this strategy identifies true bacterial clones, which are by definition genomically identical, some degree of clonal diversification may occur within patients (Walker et al. 2013...
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METHODS: Whole Genome Analysis of Genetic Alterations in Small DNA Samples Using Hyperbranched Strand Displacement Amplification and Array–CGH
- José M. Lage,
- John H. Leamon,
- Tanja Pejovic,
- Stefan Hamann,
- Michelle Lacey,
- Deborah Dillon,
- Richard Segraves,
- Bettina Vossbrinck,
- Antonio González,
- Daniel Pinkel,
- Donna G. Albertson,
- Jose Costa,
- and Paul M. Lizardi
Genome Res. February 1, 2003 13: 294-307; doi:10.1101/gr.377203
.... 2 A). Thus, although it is possible to obtain very high amplification yields with standard random primers, reactions initiated with very small inputs of genomic DNA tend to be contaminated with spurious DNA sequences. We explored the use of modified primers with one or two 5′-terminal nitroindole...

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