Searching journal content for articles similar to Alimi et al. 10 (7): 959.

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  1. 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
    ...genes (SSOGs). SSOGs cannot be explained by the insufficient sequencing of homologous sequences, because each typically contains additional genes that cannot be found in other s, as, for example, observed in Escherichia coli (Yu and Stoltzfus 2012). Also, genes specific to E. coli have been found...
  2. Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
    • Mari B. Gornitzka,
    • Egil Røsjø,
    • Uddalok Jana,
    • Easton E. Ford,
    • Alan Tourancheau,
    • William D. Lees,
    • Zachary Vanwinkle,
    • Melissa L. Smith,
    • Corey T. Watson,
    • and Andreas Lossius
    Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
    ..., France; 5Clareo Biosciences, Louisville, Kentucky 40222, USA ↵6 These authors contributed equally to this work. Corresponding authors: andreas.lossius@medisin.uio.no, corey.watson@louisville.eduAbstractGenetic diversity within the human immunoglobulin heavy-chain (IGH) locus influences the expressed...
  3. Method: Multiplexed long-read plasmid validation and analysis using OnRamp
    • Camille Mumm,
    • Melissa L. Drexel,
    • Torrin L. McDonald,
    • Adam G. Diehl,
    • Jessica A. Switzenberg,
    • and Alan P. Boyle
    Genome Res. May 2023 33: 741-749; Published in Advance May 8, 2023, doi:10.1101/gr.277369.122
    ...Escherichia coli strains.Transposase-based plasmid preparationFor transposase-based preparation, plasmids were treated using the rapid sequencing kit and following ONT's protocol (SQK-RAD004). Pooled plasmid DNA is brought to 7.5 µL using H2O, combined with 2.5 µL FRA, incubated 30°C for 1 min and then at 80...
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  4. Research: Genome-wide promoter assembly in E. coli measured at single-base resolution
    • Jordan John,
    • Javaid Jabbar,
    • Nitika Badjatia,
    • Matthew J. Rossi,
    • William K.M. Lai,
    • and B. Franklin Pugh
    Genome Res. May 2022 32: 878-892; Published in Advance April 28, 2022, doi:10.1101/gr.276544.121
    ...of the epigenomic organization of the Escherichia coli transcription machinery and nucleoid structural proteins at the time when cells are growing exponentially and upon rapid reprogramming (acute heat shock). We examined the site specificity of three sigma factors (RpoD/σ70, RpoH/σ32, and RpoN/σ54), RNA polymerase...
  5. Method: Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic
    • Jim Shaw and
    • Yun William Yu
    Genome Res. July 2023 33: 1175-1187; Published in Advance March 29, 2023, doi:10.1101/gr.277637.122
    ...to make things work better. As such, to empirically validate our theory, we implemented a basic version of sketched seed-chain-extend and tested it on simulated random sequences with independent point substitutions. For the chaining step, we implemented an AVL tree–based max-range-query method (Mäkinen et...
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  6. 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
    ...blood- or urine-derived isolates of extraintestinal pathogenic (ExPEC) Escherichia coli, a common agent of sepsis and community-acquired urinary tract infections, obtained during the course of routine clinical care at a single institution. We find that ExPEC E. coli are highly genomically heterogeneous...
  7. RESOURCE: Large-scale identification of protein–protein interaction of Escherichia coli K-12
    • Mohammad Arifuzzaman,
    • Maki Maeda,
    • Aya Itoh,
    • Kensaku Nishikata,
    • Chiharu Takita,
    • Rintaro Saito,
    • Takeshi Ara,
    • Kenji Nakahigashi,
    • Hsuan-Cheng Huang,
    • Aki Hirai,
    • Kohei Tsuzuki,
    • Seira Nakamura,
    • Mohammad Altaf-Ul-Amin,
    • Taku Oshima,
    • Tomoya Baba,
    • Natsuko Yamamoto,
    • Tomoyo Kawamura,
    • Tomoko Ioka-Nakamichi,
    • Masanari Kitagawa,
    • Masaru Tomita,
    • Shigehiko Kanaya,
    • Chieko Wada,
    • and Hirotada Mori
    Genome Res. May 2006 16: 686-691; Published in Advance April 10, 2006, doi:10.1101/gr.4527806
    ...Large-scale identification of protein–protein interaction of Escherichia coli K-12 An E. coli protein–protein interaction map Mohammad Arifuzzaman 1 , 2 , 9 , 11 , Maki Maeda 1 , 3 , 11 , Aya Itoh 4 , Kensaku Nishikata 5 , Chiharu...
  8. Research: Identification and validation of supervariants reveal novel loci associated with human white matter microstructure
    • Shiying Wang,
    • Ting Li,
    • Bingxin Zhao,
    • Wei Dai,
    • Yisha Yao,
    • Cai Li,
    • Tengfei Li,
    • Hongtu Zhu,
    • and Heping Zhang
    Genome Res. January 2024 34: 20-33; Published in Advance December 12, 2023, doi:10.1101/gr.277905.123
    .... The contributing SNPs of supervariant FXST_Chr8_25+ locate in genes NEFM and NEFL. They both show exclusive expression in the brain tissues (Fagerberg et al. 2014). NEFM encodes the neurofilament medium chain, and NEFL encodes the neurofilament light chain. Neurofilaments are essential structural scaffolding...
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  9. Research: Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131
    • Teemu Kallonen,
    • Hayley J. Brodrick,
    • Simon R. Harris,
    • Jukka Corander,
    • Nicholas M. Brown,
    • Veronique Martin,
    • Sharon J. Peacock,
    • and Julian Parkhill
    Genome Res. August 2017 27: 1437-1449; Published in Advance July 18, 2017, doi:10.1101/gr.216606.116
    ...2 0QQ, United Kingdom; 6Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom; 7British Society of Antimicrobial Chemotherapy, Birmingham B1 3NJ, United Kingdom; 8London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom Escherichia coli...
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  10. Method: Improved assembly of noisy long reads by k-mer validation
    • Antonio Bernardo Carvalho,
    • Eduardo G. Dupim,
    • and Gabriel Goldstein
    Genome Res. December 2016 26: 1710-1720; Published in Advance October 7, 2016, doi:10.1101/gr.209247.116
    ...-mer frequency distributions in PacBio and Illumina reads In order to make clear the proposed solution, we investigated in detail the data from Escherichia coli. The of E. coli strain K-12MG1655 has been sequenced and finished to high quality using Sanger reads (Blattner et al. 1997). More recently, it has been...
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