Searching journal content for articles similar to Holzerlandt et al. 12 (11): 1739.

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Method: Genome-wide CRISPR screening reveals genes essential for cell viability and resistance to abiotic and biotic stresses in Bombyx mori
- Jiasong Chang,
- Ruolin Wang,
- Kai Yu,
- Tong Zhang,
- Xiaoxu Chen,
- Yue Liu,
- Run Shi,
- Xiaogang Wang,
- Qingyou Xia,
- and Sanyuan Ma
Genome Res. May 2020 30: 757-767; Published in Advance May 18, 2020, doi:10.1101/gr.249045.119
...that are essential for cell viability under normal growth conditions. Of the identified genes, 82.4% (829 genes) were homologous to essential genes in seven animal species. We also identified 838 genes whose loss facilitated cell growth. Next, we performed context-specific positive screens for resistance to biotic...
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Research: Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion
- James Hadfield,
- Simon R. Harris,
- Helena M.B. Seth-Smith,
- Surendra Parmar,
- Patiyan Andersson,
- Philip M. Giffard,
- Julius Schachter,
- Jeanne Moncada,
- Louise Ellison,
- María Lucía Gallo Vaulet,
- Marcelo Rodríguez Fermepin,
- Frans Radebe,
- Suyapa Mendoza,
- Sander Ouburg,
- Servaas A. Morré,
- Konrad Sachse,
- Mirja Puolakkainen,
- Suvi J. Korhonen,
- Chris Sonnex,
- Rebecca Wiggins,
- Hamid Jalal,
- Tamara Brunelli,
- Patrizia Casprini,
- Rachel Pitt,
- Cathy Ison,
- Alevtina Savicheva,
- Elena Shipitsyna,
- Ronza Hadad,
- Laszlo Kari,
- Matthew J. Burton,
- David Mabey,
- Anthony W. Solomon,
- David Lewis,
- Peter Marsh,
- Magnus Unemo,
- Ian N. Clarke,
- Julian Parkhill,
- and Nicholas R. Thomson
Genome Res. July 2017 27: 1220-1229; Published in Advance June 6, 2017, doi:10.1101/gr.212647.116
...inferred recombination events each affecting selected taxa and genomic location, with color indicating the number of inferred events. Gene annotations correspond to strain D/UW3. (PZ) Plasticity zone. Hadfield et al. 1222 Genome Research www..org population of Australia showed that isolates with genotypes...
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Resource: A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
- Samia N. Naccache,
- Scot Federman,
- Narayanan Veeraraghavan,
- Matei Zaharia,
- Deanna Lee,
- Erik Samayoa,
- Jerome Bouquet,
- Alexander L. Greninger,
- Ka-Cheung Luk,
- Barryett Enge,
- Debra A. Wadford,
- Sharon L. Messenger,
- Gillian L. Genrich,
- Kristen Pellegrino,
- Gilda Grard,
- Eric Leroy,
- Bradley S. Schneider,
- Joseph N. Fair,
- Miguel A. Martínez,
- Pavel Isa,
- John A. Crump,
- Joseph L. DeRisi,
- Taylor Sittler,
- John Hackett, Jr.,
- Steve Miller,
- and Charles Y. Chiu
Genome Res. July 2014 24: 1180-1192; Published in Advance June 4, 2014, doi:10.1101/gr.171934.113
...Departamento de Gene´tica del Desarrollo y Fisiologı´a Molecular, Instituto de Biotecnologı´a, Universidad Nacional Auto´noma de Me´xico, Cuernavaca, Morelos, 62260, Mexico; 11Division of Infectious Diseases and International Health and the Duke Global Health Institute, Duke University Medical Center, Durham...
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LETTER: A Novel γ2-Herpesvirus of the Rhadinovirus 2 Lineage in Chimpanzees
- Vincent Lacoste,
- Philippe Mauclère,
- Guy Dubreuil,
- John Lewis,
- Marie-Claude Georges-Courbot,
- and Antoine Gessain
Genome Res. September 1, 2001 11: 1511-1519; doi:10.1101/gr.158601
...any other human herpesviruses than KSHV. DNA Extraction and Herpesvirus DNA Polymerase Gene Amplification DNA was extracted from buffy coats with the QIAamp DNA Blood mini kit (QIAGEN) following the manufacturer's instructions. Herpesvirus DNA polymerase gene sequences were amplified by consensus...
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Research: Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth
- Christina A. Cuomo,
- Christopher A. Desjardins,
- Malina A. Bakowski,
- Jonathan Goldberg,
- Amy T. Ma,
- James J. Becnel,
- Elizabeth S. Didier,
- Lin Fan,
- David I. Heiman,
- Joshua Z. Levin,
- Sarah Young,
- Qiandong Zeng,
- and Emily R. Troemel
Genome Res. December 2012 22: 2478-2488; Published in Advance July 18, 2012, doi:10.1101/gr.142802.112
...deep sequencing of transcripts from a time course of N. parisii infection. Examination of pathogen gene expression revealed compact transcripts and a dramatic takeover of host cells by Nematocida . We also performed phylogenomic analyses of Nematocida and other microsporidian genomes to refine...
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Method: Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End
- Lucinda C. Xiao,
- Ayush Semwal,
- Brianna St John,
- Kathleen Zeglinski,
- Shian Su,
- James Lancaster,
- Shifeng Xue,
- Bruno Reversade,
- Matthew E. Ritchie,
- Frédérique Magdinier,
- Marnie E. Blewitt,
- and Quentin Gouil
Genome Res. March 23, 2026 ; Published in Advance March 23, 2026, doi:10.1101/gr.280907.125
...4qA alleles to confirm the diagnosis of FSHD1, and identification of other structural variants whichmay contribute to FSHD pathogenesis. Cas9-targeted sequencing of 4q/10q D4Z4 alleles and FSHD2-associated genes Although ultra-longWGS is able to capture reads that span the entire 4q and 10qD4Z4...
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ARTICLE: Tropheryma whipplei Twist: A Human Pathogenic Actinobacteria With a Reduced Genome
- Didier Raoult,
- Hiroyuki Ogata,
- Stéphane Audic,
- Catherine Robert,
- Karsten Suhre,
- Michel Drancourt,
- and Jean-Michel Claverie
Genome Res. August 2003 13: 1800-1809; doi:10.1101/gr.1474603
...Tropheryma whipplei is the only known reduced genome species (&lt;1 Mb) within the Actinobacteria [high G+C Gram-positive bacteria]. We present the sequence of the 927,303-bp circular genome of T. whipplei Twist strain, encoding 808 predicted protein-coding genes. Specific genome features include...
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ARTICLE: Evolutionary Role of Restriction/Modification Systems as Revealed by Comparative Genome Analysis
- Eduardo P.C. Rocha,
- Antoine Danchin,
- and Alain Viari
Genome Res. June 1, 2001 11: 946-958; Published in Advance May 8, 2001, doi:10.1101/gr.153101
...favoring a change of emphasis on the evolutionary theory (i.e., from the action of selection units strictly at the individual level, to selection units acting at different hierarchical levels, from the gene to the group [ Gould and Lloyd 1999 ]). RESULTS Palindrome Avoidance in Bacterial Genomes We have...
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Method: Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity
- Brianna Chrisman,
- Chloe He,
- Jae-Yoon Jung,
- Nate Stockham,
- Kelley Paskov,
- Peter Washington,
- Juli Petereit,
- and Dennis P. Wall
Genome Res. October 2023 33: 1734-1746; Published in Advance October 25, 2023, doi:10.1101/gr.277175.122
...diversity, as cataloged by dbVar and the alternative sequences in the decoy. Notably, within the hotspot around Chr3:177 Mb is the repeat-containing gene TBL1XR1. Mutations in TBL1XR1 have been previously associated with autism spectrum disorders (O'Roak et al. 2012). As the iHART data set is from multiplex...
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Research: The Enterprise, a massive transposon carrying Spok meiotic drive genes
- Aaron A. Vogan,
- S. Lorena Ament-Velásquez,
- Eric Bastiaans,
- Ola Wallerman,
- Sven J. Saupe,
- Alexander Suh,
- and Hanna Johannesson
Genome Res. May 2021 31: 789-798; Published in Advance April 19, 2021, doi:10.1101/gr.267609.120
...within the . The accumulation does not appear to have been a single event but was more likely many individual events, as the genomic homologs are found on all chromosomes (green links in Fig. 2).The EnterpriseThe gene annotation provided us with very few clues as to the agent(s) responsible...
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