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Method: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
- Elisa Oberbeckmann,
- Michael Wolff,
- Nils Krietenstein,
- Mark Heron,
- Jessica L. Ellins,
- Andrea Schmid,
- Stefan Krebs,
- Helmut Blum,
- Ulrich Gerland,
- and Philipp Korber
Genome Res. December 2019 29: 1996-2009; Published in Advance November 6, 2019, doi:10.1101/gr.253419.119
...(Thermo Fisher Scientific) against 15 mL methylation buffer with 200 µM freshly added SAM at 25°C for M.SssI or 37°C for M.CviPI. Next, 0.5–1 µg fully assembled pUC19-601-25mer plasmid (pFMP233) (Lowary and Widom 1998; Lieleg et al. 2015a) and Saccharomyces Genome Database (SGD) assembled Escherichia coli...
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LETTER: Engineering a Reduced Escherichia coli Genome
- Vitaliy Kolisnychenko,
- Guy Plunkett III,
- Christopher D. Herring,
- Tamás Fehér,
- János Pósfai,
- Frederick R. Blattner,
- and György Pósfai
Genome Res. April 1, 2002 12: 640-647; doi:10.1101/gr.217202
....F. , Evans P.S. , Gregor J. , Kirkpatrick H.A. , et al. ( 2001 ) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409 : 529 – 533 . ↵ Pósfai G. , Koob M.D. , Kirkpatrick H.A. , Blattner F.R. ( 1997 ) Versatile insertion plasmids for targeted manipulations in bacteria: Isolation...
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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
...apply StrainPGC to metas from a clinical trial of fecal microbiota transplantation for the treatment of ulcerative colitis. We identify two Escherichia coli strains, from two different donors, that are both frequently transmitted to patients but have notable differences in functional potential. Strain...
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Research: Genome-wide detection of novel regulatory RNAs in E. coli
- Rahul Raghavan,
- Eduardo A. Groisman,
- and Howard Ochman
Genome Res. September 2011 21: 1487-1497; Published in Advance June 10, 2011, doi:10.1101/gr.119370.110
...regulatory leader sequences and small RNAs (sRNAs), which both serve to modulate gene expression. Computational analyses have predicted the presence of hundreds of these noncoding regulatory RNAs in Escherichia coli ; however, only about 80 have been experimentally validated. By applying a deep...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...translation. Complete -wide ChIP-seq for a TF can be mapped within the cells and tissues in an efficient and timely manner with novel technologies.However, complications arise when we pose the DNA-centric question: which proteins are bound to, and directly regulate, a GOI. Initial approaches consisted...
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Research: Proteome-wide structural analysis quantifies structural conservation across distant species
- Shijie Zhang,
- Teng Zhang,
- and Yuan Fu
Genome Res. November 2023 33: 1975-1993; Published in Advance November 22, 2023, doi:10.1101/gr.277771.123
...-wide structural analysis using experimental and computed protein structures for organisms from the three distinct domains, including Homo sapiens (eukarya), Escherichia coli (bacteria), and Methanocaldococcus jannaschii (archaea). We reveal the distribution of structural similarity and sequence identity...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...be entirely complete and accurate. Partly for that reason, attempts at such synthetic biology have focused heavily until now on modifying the s of single-celled organisms, such as the bacterium Escherichia coli or the baker's yeast S. cerevisiae (Pelletier et al. 2021; Zhao et al. 2023; Tian et al. 2024...
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Research: Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts
- Isabela T. Pereira,
- Izabela Mamede,
- Paulo P. Amaral,
- Gloria R. Franco,
- and John L. Rinn
Genome Res. October 2025 35: 2189-2198; Published in Advance August 26, 2025, doi:10.1101/gr.280431.125
...of a particular RNA in cell extract (red) and in purified total RNA (blue). (B) Heat map representing the abundance (normalized counts) of RNA transcripts in each gradient fraction of cell extracts and purified RNA gradients. Columns are gradient fractions; rows are RNA transcripts. (C) Examples of GETs...
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Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...then leverage the length of long reads by finding walks along the PDBG through unitig construction and read-to-graph alignment. We find that devider efficiently resolves haplotypes in a variety of synthetic and real data sets and show its versatility to reveal genomic heterogeneity.MethodsAt a high level...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...and Escherichia coli (Shao et al. 2020). Other databases are focused only on a small set of species or are providing a set of experimentally validated G4s (Li et al. 2013; Ghosh et al. 2021; Wang et al. 2022; Zok et al. 2022; Qian et al. 2024), yet none of these databases contain a wide range of s, representing...
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