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Resource: Inversion variants in human and primate genomes
- Claudia Rita Catacchio,
- Flavia Angela Maria Maggiolini,
- Pietro D'Addabbo,
- Miriana Bitonto,
- Oronzo Capozzi,
- Martina Lepore Signorile,
- Mattia Miroballo,
- Nicoletta Archidiacono,
- Evan E. Eichler,
- Mario Ventura,
- and Francesca Antonacci
Genome Res. May 18, 2018 ; Published in Advance May 18, 2018, doi:10.1101/gr.234831.118
...in the references has immediate applications for evolutionary and biomedical studies on primates. [Supplemental material is available for this article.] A long-standing question in evolutionary biology concerns the effect of inversions in shaping the genomic architecture of organisms. The most conspicuous...
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Research: Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus
- Julie E. Horvath,
- Christina B. Sheedy,
- Stephanie L. Merrett,
- Abdoulaye Banire Diallo,
- David L. Swofford,
- NISC Comparative Sequencing Program,
- Eric D. Green,
- and Huntington F. Willard
Genome Res. June 2011 21: 850-862; Published in Advance April 25, 2011, doi:10.1101/gr.111849.110
...in overall sequence identity and short repeat insertions. While this comparative analysis reinforces that the region around XIST has been subject to significant genomic change, even among primates, our data suggest that evolution of the XIST sequences themselves represents only small lineage...
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Method: The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells
- Mireia Jordà,
- Anna Díez-Villanueva,
- Izaskun Mallona,
- Berta Martín,
- Sergi Lois,
- Víctor Barrera,
- Manel Esteller,
- Tanya Vavouri,
- and Miguel A. Peinado
Genome Res. January 2017 27: 118-132; Published in Advance December 20, 2016, doi:10.1101/gr.207522.116
...instability. Our analysis demonstrates that Alu retroelements contribute to define the epigenetic landscape of normal and cancer cells and provides a unique resource on the epigenetic dynamics of a principal, but largely unexplored, component of the primate . Cancer cells are characterized by the acquisition...
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LETTER: Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome
- Ge Liu,
- NISC Comparative Sequencing Program,
- Shaying Zhao,
- Jeffrey A. Bailey,
- S. Cenk Sahinalp,
- Can Alkan,
- Eray Tuzun,
- Eric D. Green,
- and Evan E. Eichler
Genome Res. March 1, 2003 13: 358-368; doi:10.1101/gr.923303
...evolution: A proposal for a primate genomic library resource. Genome Res. 12 : 673 – 678 . ↵ Felsenfeld A. , Peterson J. , Schloss J. , Guyer M. ( 1999 ) Assessing the quality of the DNA sequence from the Human Genome Project. Genome Res. 9 : 1 – 4 . ↵ Fujiyama A. , Watanabe H. , Toyoda A. , Taylor T...
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Resource: Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment
- Martin Ebeling,
- Erich Küng,
- Angela See,
- Clemens Broger,
- Guido Steiner,
- Marco Berrera,
- Tobias Heckel,
- Leonardo Iniguez,
- Thomas Albert,
- Roland Schmucki,
- Hermann Biller,
- Thomas Singer,
- and Ulrich Certa
Genome Res. October 2011 21: 1746-1756; Published in Advance August 23, 2011, doi:10.1101/gr.123117.111
...;gr.123117.111 1088-9051 Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment Resource Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment Martin Ebeling,1 Erich Ku¨ng,2 Angela See,3 Clemens Broger,4 Guido...
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Methods: Pooled genomic indexing of rhesus macaque
- Aleksandar Milosavljevic,
- Ronald A. Harris,
- Erica J. Sodergren,
- Andrew R. Jackson,
- Ken J. Kalafus,
- Anne Hodgson,
- Andrew Cree,
- Weilie Dai,
- Miklos Csuros,
- Baoli Zhu,
- Pieter J. de Jong,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. February 2005 15: 292-301; doi:10.1101/gr.3162505
...organisms, direct study of haplotype structure within populations, and disease-causing germline rearrangements characteristic of genomic disorders ( Lupski 1998 ). A newly proposed end-sequence profiling (ESP) method ( Raphael et al. 2003 ; Volik et al. 2003 ) extends applications to the somatic level...
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ARTICLE: Large-Scale Variation Among Human and Great Ape Genomes Determined by Array Comparative Genomic Hybridization
- Devin P. Locke,
- Richard Segraves,
- Lucia Carbone,
- Nicoletta Archidiacono,
- Donna G. Albertson,
- Daniel Pinkel,
- and Evan E. Eichler
Genome Res. March 1, 2003 13: 347-357; doi:10.1101/gr.1003303
...A. , Ecale Zhou C.L. , Rash S. , et al. ( 2001 ) Human chromosome 19 and related regions in mouse: Conservative and lineage-specific evolution. Science 293 : 104 – 111 . ↵ Eichler E.E. , DeJong P.J. ( 2002 ) Biomedical applications and studies of molecular evolution: A proposal for a primate genomic...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...lines and strains, and a high rate of gene retroposition. Our study offers novel insights into mammalian evolution and highlights the importance of repetitive elements in shaping genomic diversity.All forms of genetic variation originate from new mutations, so it is important to know the rate at which...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...decayed during early primate evolution (>50 million years ago [MYA]) before stabilizing since the separation of Old World monkeys (<50 MYA). Taken together, our results suggest ancient and lineage-specific transposon subfamilies contributed to mammalian NF-kB regulatory networks.Transposable elements (TEs...
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Method: Marker-free characterization of full-length transcriptomes of single live circulating tumor cells
- Sarita Poonia,
- Anurag Goel,
- Smriti Chawla,
- Namrata Bhattacharya,
- Priyadarshini Rai,
- Yi Fang Lee,
- Yoon Sim Yap,
- Jay West,
- Ali Asgar Bhagat,
- Juhi Tayal,
- Anurag Mehta,
- Gaurav Ahuja,
- Angshul Majumdar,
- Naveen Ramalingam,
- and Debarka Sengupta
Genome Res. January 2023 33: 80-95; Published in Advance November 22, 2022, doi:10.1101/gr.276600.122
...27701, USA; 13Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117575, Singapore; 14Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore Corresponding authors: debarka...

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