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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...the local genomic environment. To experimentally validate these observations, we conducted in situ RNA hybridization using a probe designed against the pol gene of ERV1-3 on embryos at the three-somite stage (11 hpf). As a comparison, we also performed in situ hybridization with a probe for foxc1a...
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Research: Genomic analysis of circulating cell-free DNA infers breast cancer dormancy
- Jacqueline A. Shaw,
- Karen Page,
- Kevin Blighe,
- Natasha Hava,
- David Guttery,
- Becky Ward,
- James Brown,
- Chetana Ruangpratheep,
- Justin Stebbing,
- Rachel Payne,
- Carlo Palmieri,
- Suzy Cleator,
- Rosemary A. Walker,
- and R. Charles Coombes
Genome Res. February 2012 22: 220-231; Published in Advance October 11, 2011, doi:10.1101/gr.123497.111
...DNA) isolated from plasma may form the basis for a means of detecting and monitoring breast cancer. We profiled 251 genomes using Affymetrix SNP 6.0 arrays to determine copy number variations (CNVs) and loss of heterozygosity (LOH), comparing 138 cfDNA samples with matched primary tumor and normal leukocyte DNA...
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Research: Genomic, proteomic, and transcriptomic analysis of virulent and avirulent Rickettsia prowazekii reveals its adaptive mutation capabilities
- Yassina Bechah,
- Khalid El Karkouri,
- Oleg Mediannikov,
- Quentin Leroy,
- Nicolas Pelletier,
- Catherine Robert,
- Claudine Médigue,
- Jean-Louis Mege,
- and Didier Raoult
Genome Res. May 2010 20: 655-663; Published in Advance April 5, 2010, doi:10.1101/gr.103564.109
.... Transcriptional and proteomic analyses of R. prowazekii surface protein expression and protein methylation varied with virulence. By sequencing a virulent strain and using comparative genomics, we found hotspots of mutations in homopolymeric tracts of poly(A) and poly(T) in eight genes in an avirulent strain...
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LETTER: High-resolution Genetic and Physical Map of the Lgn1 Interval in C57BL/6J Implicates Naip2 or Naip5 in Legionella pneumophila Pathogenesis
- Joseph D. Growney and
- William F. Dietrich
Genome Res. August 1, 2000 10: 1158-1171; doi:10.1101/gr.10.8.1158
...allow us to improve our genetic mapping of Lgn1 . Our interest in understanding both the mechanisms involved in the apparent genomic instability of this region and in identifying the Lgn1 gene have led us to compare the structure of the Naip array among commonly used inbred mouse strains. Here, we...
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RESEARCH: Cloning, Characterization, and Copy Number of the Murine Survival Motor Neuron Gene: Homolog of the Spinal Muscular Atrophy-Determining Gene
- Christine J. DiDonato,
- Xiao-Ning Chen,
- David Noya,
- Julie R. Korenberg,
- Joseph H. Nadeau,
- and Louise R. Simard
Genome Res. April 1, 1997 7: 339-352; doi:10.1101/gr.7.4.339
...the mouse genome, which should facilitate gene disruption experiments to create an animal model of SMA. [The murine Smn cDNA sequence has been submitted to GenBank under accession no. U77714 . The Mouse Genome Database accession no. for FISH mapping of Smn and Naip is MGD-INEX-31 and for the genetic...
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LETTER: Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene Clusters
- Qiang Wu,
- Theresa Zhang,
- Jan-Fang Cheng,
- Youngwook Kim,
- Jane Grimwood,
- Jeremy Schmutz,
- Mark Dickson,
- James P. Noonan,
- Michael Q. Zhang,
- Richard M. Myers,
- and Tom Maniatis
Genome Res. March 1, 2001 11: 389-404; doi:10.1101/gr.167301
.... Remarkably, the variable 5′ region of each human protocadherin cDNA was found to be encoded by a different large exon, and the variable region exons are organized in a tandem array in each gene cluster. Sequence comparisons of genomic DNA and cDNAs identified three small exons downstream from Pcdh α and Pcdh...
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PERSPECTIVE: Using Mouse Genetics to Understand Infectious Disease Pathogenesis
- William F. Dietrich
Genome Res. March 1, 2001 11: 325-331; doi:10.1101/gr.173101
...) Genomic sequence analysis of the mouse Naip gene array. Genome Res. 10 : 1095 – 1102 . ↵ Fang G.D. , Fine M. , Orloff J. , Arisumi D. , Yu V.L. , Kapoor W. , Grayston J.T. , Wang S.P. , Kohler R. , Muder R.R. , et al. ( 1990 ) New and emerging etiologies for community-acquired pneumonia with implications...
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Research: Extensive relationship between antisense transcription and alternative splicing in the human genome
- A. Sorana Morrissy,
- Malachi Griffith,
- and Marco A. Marra
Genome Res. August 2011 21: 1203-1212; Published in Advance June 30, 2011, doi:10.1101/gr.113431.110
...lines represent equal proportions of SAS genes or antisense ESTs among genes with multiple or single isoforms. Note that some organisms have very few ESTs (see Supplemental Table 4B). Antisense-correlated alternative splicing Genome Research 1209 www..org The use of exon arrays in this work reflects...
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LETTER: Comparative Analysis of Apoptosis and Inflammation Genes of Mice and Humans
- John C. Reed,
- Kutbuddin Doctor,
- Ana Rojas,
- Juan M. Zapata,
- Christian Stehlik,
- Loredana Fiorentino,
- Jason Damiano,
- Wilfried Roth,
- Shu-ichi Matsuzawa,
- Ruchi Newman,
- Shinichi Takayama,
- Hiroyuki Marusawa,
- Famming Xu,
- Guy Salvesen,
- RIKEN GER Group,
- GSL Members,
- and Adam Godzik
Genome Res. June 2003 13: 1376-1388; doi:10.1101/gr.1053803
...) databases, we compared the repertoire of apoptosis and NFκB-inducing genes in humans and mice from cDNA/EST/genomic data, focusing on the following domain families: (1) Caspase proteases; (2) Caspase recruitment domains (CARD); (3) Death Domains (DD); (4) Death Effector Domains (DED); (5) BIR domains...
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ARTICLE: Sequence and Comparative Analysis of the Mouse 1-Megabase Region Orthologous to the Human 11p15 Imprinted Domain
- Patrick Onyango,
- Webb Miller,
- Jessica Lehoczky,
- Cheuk T. Leung,
- Bruce Birren,
- Sarah Wheelan,
- Ken Dewar,
- and Andrew P. Feinberg
Genome Res. November 1, 2000 10: 1697-1710; doi:10.1101/gr.161800
...organization of genes and of the potentially important cis -acting regulatory sequences that lie in the nonexonic segments that make up 97% of the genome. Interspecies sequence comparison offers an effective approach to identify sequence from conserved functional elements. In this article we describe...

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