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Resource: An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- Chong Li,
- Marc Jan Bonder,
- Sabriya Syed,
- Matthew Jensen,
- Human Genome Structural Variation Consortium (HGSVC),
- HGSVC Functional Analysis Working Group,
- Mark B. Gerstein,
- Michael C. Zody,
- Mark J.P. Chaisson,
- Michael E. Talkowski,
- Tobias Marschall,
- Jan O. Korbel,
- Evan E. Eichler,
- Charles Lee,
- and Xinghua Shi
Genome Res. December 2024 34: 2304-2318; Published in Advance December 5, 2024, doi:10.1101/gr.279419.124
...An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human s Chong Li1,2, Marc Jan Bonder3,4, Sabriya Syed5, Matthew Jensen6,7, Human Genome Structural Variation Consortium (HGSVC), HGSVC Functional Analysis Working Group, Mark B...
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Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
...histone modification in sperm indicates that sperm DNA methylation is an integral part of the germline epi evolution.View larger version: In this window In a new window Figure 5. Sperm DNA methylation divergence is accompanied by sperm histone modification and DNA sequence divergence. (A) Mouse- and human-specific...
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Research: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
- Baoxing Song,
- Edward S. Buckler,
- Hai Wang,
- Yaoyao Wu,
- Evan Rees,
- Elizabeth A. Kellogg,
- Daniel J. Gates,
- Merritt Khaipho-Burch,
- Peter J. Bradbury,
- Jeffrey Ross-Ibarra,
- Matthew B. Hufford,
- and M. Cinta Romay
Genome Res. July 2021 31: 1245-1257; Published in Advance May 27, 2021, doi:10.1101/gr.266528.120
...alignment pipeline to identify conserved noncoding sequences (CNSs) in the Andropogoneae tribe (multiple crop species descended from a common ancestor ∼18 million years ago). The Andropogoneae share similar physiology while being tremendously genomically diverse, harboring a broad range of ploidy levels...
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Method: The multicomparative 2-n-way genome suite
- Gennady Churakov,
- Fengjun Zhang,
- Norbert Grundmann,
- Wojciech Makalowski,
- Angela Noll,
- Liliya Doronina,
- and Jürgen Schmitz
Genome Res. October 2020 30: 1508-1516; Published in Advance July 29, 2020, doi:10.1101/gr.262261.120
...informative retrotransposon markers, activity patterns of retrotransposons, and other genomic insertions/deletions (Schmitz et al. 2016), and it was recently used to systematically screen for retrotransposon presence/absence homoplasy cases (Doronina et al. 2019). However, one significant limitation of GPAC...
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Letter: Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions
- Erika M. Kvikstad,
- Francesca Chiaromonte,
- and Kateryna D. Makova
Genome Res. July 2009 19: 1153-1164; Published in Advance June 5, 2009, doi:10.1101/gr.088922.108
...by unique enrichment profiles in the vicinity of indels vs. indel-free portions of the genome, verifying the importance of sequence context in indel mutagenesis. Second, only limited similarity in motif frequency profiles is evident flanking insertions vs. deletions, confirming differences...
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Method: Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
- Michael F. Lin,
- Pouya Kheradpour,
- Stefan Washietl,
- Brian J. Parker,
- Jakob S. Pedersen,
- and Manolis Kellis
Genome Res. November 2011 21: 1916-1928; Published in Advance October 12, 2011, doi:10.1101/gr.108753.110
...Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes Michael F. Lin 1 , 2 , Pouya Kheradpour 1 , 2 , Stefan Washietl 2 , Brian J. Parker 3 , Jakob S. Pedersen 3 , 5...
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Perspective: Reading TE leaves: New approaches to the identification of transposable element insertions
- David A. Ray and
- Mark A. Batzer
Genome Res. June 2011 21: 813-820; doi:10.1101/gr.110528.110
...and publication date are at http://www..org/cgi/doi/ 10.1101/gr.110528.110. 21:813–820 2011 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/11; www..org Genome Research 813 www..org Element 1, L1),Alu, and SVAhave insertions that are human specific and many that are recent enough to still be polymorphic...
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Research: A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis
- Pengfei Cai,
- Auke B.C. Otten,
- Binbin Cheng,
- Mitsuhiro A. Ishii,
- Wen Zhang,
- Beibei Huang,
- Kun Qu,
- and Bryan K. Sun
Genome Res. January 2020 30: 22-34; Published in Advance December 4, 2019, doi:10.1101/gr.251561.119
...(Quek et al. 2015). This is in part due to the challenges of studying lncRNAs. They are less sequence-conserved than proteins (Kellis et al. 2014), and some functional lncRNAs are primate- or even human-specific (Awan et al. 2017). This limits the application of classical genetic systems, such as murine...
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Method: Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations
- David J. Witherspoon,
- Yuhua Zhang,
- Jinchuan Xing,
- W. Scott Watkins,
- Hongseok Ha,
- Mark A. Batzer,
- and Lynn B. Jorde
Genome Res. July 2013 23: 1170-1181; Published in Advance April 18, 2013, doi:10.1101/gr.148973.112
...are the most numerous and active mobile elements in humans, causing genetic disease and creating genomic diversity. Mobile element scanning (ME-Scan) enables comprehensive and affordable identification of mobile element insertions (MEI) using targeted high-throughput sequencing of multiplexed MEI junction...
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Research: Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
- Nathan H. Lazar,
- Kimberly A. Nevonen,
- Brendan O'Connell,
- Christine McCann,
- Rachel J. O'Neill,
- Richard E. Green,
- Thomas J. Meyer,
- Mariam Okhovat,
- and Lucia Carbone
Genome Res. July 2018 28: 983-997; Published in Advance June 18, 2018, doi:10.1101/gr.233874.117
...of inversions) or on two different human chromosomes (in the case of translocations, fissions, or fusions). The human was selected to represent the ancestral hominoid because of its unmatched quality among primate assemblies. The rhesus macaque was used to discriminate human-specific and great ape-specific from...

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