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Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
...k-mer cross-species profiling reveals taxon-specific TE expansions accompanied 1 by KZFP co-option and functional impacts in ruminants 2 3 Pengju Zhao1,2*, Jiayi He1,2, Chen Peng1,2, Yuelang Zhang1,2, Chong Wang1,2, 4 Dongyou Yu1,2, Lingzhao Fang3*, Zhengguang Wang1,2* 5 6 1Hainan Institute...
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Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
- Sudeshna Majumdar,
- Lakshmi Sowjanya Bammidi,
- Hemant C. Naik,
- Avinchal Manhas,
- Runumi Baro,
- Akash Kalita,
- Amlan Jyoti Naskar,
- Sundarraj Nidharshan,
- Girija S. Bariha,
- Dimple Notani,
- and Srimonta Gayen
Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
...data set of MEF cells with random XCI (Supplemental Table S1; Du et al. 2024). We found that the Xist and Ftx locus in MEF cells also flanked by CTCF and cohesins, like XEN cells (Supplemental Fig. S1D). Next, we profiled the enrichment of H3K27ac and H3K4me1 in the Xist upstream regulatory region...
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Method: Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
- Joseph W. Foley,
- Chunfang Zhu,
- Philippe Jolivet,
- Shirley X. Zhu,
- Peipei Lu,
- Michael J. Meaney,
- and Robert B. West
Genome Res. November 2019 29: 1816-1825; Published in Advance September 13, 2019, doi:10.1101/gr.234807.118
...with the tumor microenvironment. We propose Smart-3SEQ as a highly cost-effective method to enable large gene expression profiling experiments unconstrained by sample size and tissue availability. In particular, Smart-3SEQ's compatibility with FFPE tissue unlocks an enormous number of archived clinical samples...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...of WormBase genes overlapping with Trinity assembled transcripts. (B) Bar chart depicts contributions of individual features to the random forest models of GF and GG. A detailed description of features and their sources is provided in Supplemental Table S4. (C) 2D kernel density plots of the observed...
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Methods: A Versatile Assay for High-Throughput Gene Expression Profiling on Universal Array Matrices
- Jian-Bing Fan,
- Joanne M. Yeakley,
- Marina Bibikova,
- Eugene Chudin,
- Eliza Wickham,
- Jing Chen,
- Dennis Doucet,
- Philippe Rigault,
- Baohong Zhang,
- Richard Shen,
- Celeste McBride,
- Hai-Ri Li,
- Xiang-Dong Fu,
- Arnold Oliphant,
- David L. Barker,
- and Mark S. Chee
Genome Res. May 2004 14: 878-885; doi:10.1101/gr.2167504
...and tag microarrays. Nucleic Acids. Res. 31 : e103 . ↵ Barker, D.L., Theriault, G., Che, D., Dickinson, T. Shen, R., and Kain, R. 2003 . Self-assembled random arrays: High-performance imaging and genomics applications on a high-density microarray platform. Proc. SPIE 4966 : 1 -11. ↵ Chuaqui, R.F., Bonner...
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Research: Sex-biased genetic effects on gene regulation in humans
- Antigone S. Dimas,
- Alexandra C. Nica,
- Stephen B. Montgomery,
- Barbara E. Stranger,
- Towfique Raj,
- Alfonso Buil,
- Thomas Giger,
- Tuuli Lappalainen,
- Maria Gutierrez-Arcelus,
- MuTHER Consortium,
- Mark I. McCarthy,
- and Emmanouil T. Dermitzakis
Genome Res. December 2012 22: 2368-2375; Published in Advance September 7, 2012, doi:10.1101/gr.134981.111
..., Chee MS. 2004. A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res 14: 2347–2356. McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A, et al. 2010. Heritable individual-specific and allele...
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Methods: High-throughput DNA methylation profiling using universal bead arrays
- Marina Bibikova,
- Zhenwu Lin,
- Lixin Zhou,
- Eugene Chudin,
- Eliza Wickham Garcia,
- Bonnie Wu,
- Dennis Doucet,
- Neal J. Thomas,
- Yunhua Wang,
- Ekkehard Vollmer,
- Torsten Goldmann,
- Carola Seifart,
- Wei Jiang,
- David L. Barker,
- Mark S. Chee,
- Joanna Floros,
- and Jian-Bing Fan
Genome Res. March 2006 16: 383-393; Published in Advance January 31, 2006, doi:10.1101/gr.4410706
...of cancer. Nat. Genet. 33 Suppl: 238 –244. ↵ Barker, D.L., Theriault, G., Che, D., Dickinson, T., Shen, R., and Kain, R. 2003 . Self-assembled random arrays: High-performance imaging and genomics applications on a high-density microarray platform. Proc. SPIE 4966 : 1 –11. ↵ Baylin, S.B. and Herman, J...
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Method: High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection
- Sara J. Cooper,
- Gregory L. Finney,
- Shauna L. Brown,
- Sven K. Nelson,
- Jay Hesselberth,
- Michael J. MacCoss,
- and Stanley Fields
Genome Res. September 2010 20: 1288-1296; Published in Advance July 7, 2010, doi:10.1101/gr.105825.110
...spectrometry, high-performance liquid chromatography, and nuclear magnetic resonance studies are time intensive, so far precluding their use to assay thousands of samples on a single platform. However, smaller scale studies have demonstrated the utility of measuring metabolite levels in yeast, worms, and other...
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Methods: Development of a microscopic platform for real-time monitoring of biomolecular interactions
- Yasuhiro Sasuga,
- Tomomi Tani,
- Masahito Hayashi,
- Hisashi Yamakawa,
- Osamu Ohara,
- and Yoshie Harada
Genome Res. January 2006 16: 132-139; Published in Advance December 12, 2005, doi:10.1101/gr.4235806
...μm area), and TIRFM made it possible to monitor the binding reactions of fluorescently labeled targets onto probe microbeads without removal of free targets. We demonstrated the high performance of this platform through analyses of interactions between antigen and antibody and between small compounds...
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Methods: RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
- John C. Marioni,
- Christopher E. Mason,
- Shrikant M. Mane,
- Matthew Stephens,
- and Yoav Gilad
Genome Res. September 2008 18: 1509-1517; Published in Advance June 11, 2008, doi:10.1101/gr.079558.108
...of the Illumina sequencing (formerly Solexa sequencing) platform to study mRNA expression levels. Our goals were to estimate technical variance associated with Illumina sequencing in this context and to compare its ability to identify differentially expressed genes with existing array technologies. To do so, we...
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