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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...hypersensitivity), high nucleosomal turnover (e.g., high levels of rapid-turnover histones H2A.Z and H3.3), specific epigenetic markers (e.g., high ratio of H3K4me1 and H3K4me2 to H3K4me3, high ratio of 5hmC to 5mC, enrichment of H3K27ac), chromatin loops in direct contact with the core promoter (enrichment...
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Research: Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts
- Catherine Lozupone,
- Karoline Faust,
- Jeroen Raes,
- Jeremiah J. Faith,
- Daniel N. Frank,
- Jesse Zaneveld,
- Jeffrey I. Gordon,
- and Rob Knight
Genome Res. October 2012 22: 1974-1984; Published in Advance June 4, 2012, doi:10.1101/gr.138198.112
...others are universal. Biological properties that plant and microbial opportunists may share include rapid growth on limiting or labile (evanescent) resources (McCook 1994; Sigler and Zeyer 2004; Fierer et al. 2010; Vieira-Silva and Rocha 2010), high-dispersal capabilities facilitated by cosmopolitan...
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Method: Defining cell-type specificity at the transcriptional level in human disease
- Wenjun Ju,
- Casey S. Greene,
- Felix Eichinger,
- Viji Nair,
- Jeffrey B. Hodgin,
- Markus Bitzer,
- Young-suk Lee,
- Qian Zhu,
- Masami Kehata,
- Min Li,
- Song Jiang,
- Maria Pia Rastaldi,
- Clemens D. Cohen,
- Olga G. Troyanskaya,
- and Matthias Kretzler
Genome Res. November 2013 23: 1862-1873; Published in Advance August 15, 2013, doi:10.1101/gr.155697.113
...relied on mouse (Endlich et al. 2002; Brunskill et al. 2011; Jain et al. 2011) or human (Saleem et al. 2008) immortalized glomerular visceral epithelial cells, but in vitro culture leads to rapid loss of both lineagespecific phenotypes and lineage-specific gene expression. Wholetissue–based molecular...
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RESOURCE: An initial map of insertion and deletion (INDEL) variation in the human genome
- Ryan E. Mills,
- Christopher T. Luttig,
- Christine E. Larkins,
- Adam Beauchamp,
- Circe Tsui,
- W. Stephen Pittard,
- and Scott E. Devine
Genome Res. September 2006 16: 1182-1190; Published in Advance August 10, 2006, doi:10.1101/gr.4565806
....R. , Yeh R.T. , Gish W.R. , Waterston R.H. , Plasterk R.H.A. ( 2001 ) Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map . Nat. Genet. 28 : 160 – 164 . An initial map of insertion and deletion (INDEL) variation in the human Ryan E. Mills 1 , 2 , Christopher T. Luttig 1...
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Methods: Identification of novel mammalian growth regulatory factors by genome-scale quantitative image analysis
- Josephine N. Harada,
- Kristen E. Bower,
- Anthony P. Orth,
- Scott Callaway,
- Christian G. Nelson,
- Casey Laris,
- John B. Hogenesch,
- Peter K. Vogt,
- and Sumit K. Chanda
Genome Res. August 2005 15: 1136-1144; Published in Advance July 15, 2005, doi:10.1101/gr.3889305
...through -level computational image analysis. Over the last decade, the rapid expansion in sequence has led to the identification of genes at a rate that far exceeds the capacity to understand their function ( Adams et al. 2000 ; Lander et al. 2001 ; Venter et al. 2001 ; Waterston et al. 2002 ; Gibbs et al...
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REVIEW: Copy number variation: New insights in genome diversity
- Jennifer L. Freeman,
- George H. Perry,
- Lars Feuk,
- Richard Redon,
- Steven A. McCarroll,
- David M. Altshuler,
- Hiroyuki Aburatani,
- Keith W. Jones,
- Chris Tyler-Smith,
- Matthew E. Hurles,
- Nigel P. Carter,
- Stephen W. Scherer,
- and Charles Lee
Genome Res. August 2006 16: 949-961; Published in Advance June 29, 2006, doi:10.1101/gr.3677206
.... Array-based comparative genomic experiments (e.g., array CGH) have also been shown to be valuable for discovering CNVs. Advantages of array-based CGH approaches include cost effectiveness and rapid screening of numerous individuals with a given platform, but clearly the resolution is limited by the size...
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LETTER: A Genomic Analysis of Rat Proteases and Protease Inhibitors
- Xose S. Puente and
- Carlos López-Otín
Genome Res. April 2004 14: 609-622; doi:10.1101/gr.1946304
...expressed in spermatogonia ( Wang et al. 2001 ), likely playing a reproductive function and being subjected to strong selection pressures that lead to its rapid evolution ( Swanson and Vacquier 2002 ). Similar to the case of USPs, the C48 family of sentrin/SUMO-specific proteases (SENPs) also exhibits...
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ARTICLE: A gene-rich cluster between the CD4 and triosephosphate isomerase genes at human chromosome 12p13.
- M A Ansari-Lari,
- D M Muzny,
- J Lu,
- F Lu,
- C E Lilley,
- S Spanos,
- T Malley,
- and R A Gibbs
Genome Res. April 1996 6: 314-326; doi:10.1101/gr.6.4.314
....A. Edwards, M.C., Clemens, P.R. Tristan, M. Pizzuti, A. and Gibbs. R.A. 1991 . Pentanucleotide repeat length polymorphism at the human CD4 locus. Nucleic Acids Res. 19 : 4791 . Frohman, M.A., , Dush, M.K. , Martin. G.R. Frohman, M.A., Dush, M.K. and Martin. G.R. 1988 . Rapid production of full-length c...
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Letter: Alternative Gene Form Discovery and Candidate Gene Selection from Gene Indexing Projects
- John Burke,
- Hui Wang,
- Winston Hide,
- and Daniel B. Davison
Genome Res. March 1, 1998 8: 276-290; doi:10.1101/gr.8.3.276
...inconsistent (unalignable) regions into a cluster and inconsistent sequences can be partitioned into disparate subclusters. In addition to increasing the sensitivity of expression studies, the subpartition provides a rapid method of screening regulated alternative splicing vesus constitutive splicing. Figure 5...

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