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Methods: A Rapid Method of Genomic Array Analysis of Scaffold/Matrix Attachment Regions (S/MARs) Identifies a 2.5-Mb Region of Enhanced Scaffold/Matrix Attachment at a Human Neocentromere
- Huseyin Sumer,
- Jeffrey M. Craig,
- Mandy Sibson,
- and K.H. Andy Choo
Genome Res. July 2003 13: 1737-1743; doi:10.1101/gr.1095903
...chromosome scaffolds. J. Cell. Biol. 100 : 1706 -1715. ↵ Frisch, M., Frech, K., Klingenhoff, A., Cartharius, K., Liebich, I., and Werner, T. 2002 . In silico prediction of scaffold/matrix attachment regions in large genomic sequences. Genome Res. 12 : 349 -354. ↵ Galande, S. and Kohwi-Shigematsu, T. 1999...
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Methods: Generic eukaryotic core promoter prediction using structural features of DNA
- Thomas Abeel,
- Yvan Saeys,
- Eric Bonnet,
- Pierre Rouzé,
- and Yves Van de Peer
Genome Res. February 2008 18: 310-323; Published in Advance December 20, 2007, doi:10.1101/gr.6991408
...cluster varied greatly for the different properties, which again indicates that the different properties contain complementary information. Bode et al. (2006) have shown that it is very hard to identify scaffold/matrix attachment regions (SMARs) from the sequence, as the important scaffold proteins...
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LETTER: Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex
- Diego Ottaviani,
- Elliott Lever,
- Richard Mitter,
- Tania Jones,
- Tim Forshew,
- Rossitza Christova,
- Eleni M. Tomazou,
- Vardhman K. Rakyan,
- Stephen A. Krawetz,
- Adrian E. Platts,
- Badmavady Segarane,
- Stephan Beck,
- and Denise Sheer
Genome Res. November 2008 18: 1778-1786; Published in Advance October 10, 2008, doi:10.1101/gr.082313.108
...: 155 – 161 . ↵ Heng, H.H. , Goetze, S. , Ye, C.J. , Liu, G. , Stevens, J.B. , Bremer, S.W. , Wykes, S.M. , Bode, J. , Krawetz, S.A. ( 2004 ) Chromatin loops are selectively anchored using scaffold/matrix-attachment regions . J. Cell Sci. 117 : 999 – 1008 . ↵ Horton, R. , Wilming, L. , Rand, V...
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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
...in silico is challenging; researchers often analyze an arbitrary sequence length surrounding the TSS or rely on database-mined experimental data. Sequence conservation analysis can help identify important regulatory sequences (Stark et al. 2007).At least 40%–50% of human genes are subject to some degree...
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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
...homology and in silico structural prediction. The first gene encodes a tyrosine recombinase/integrase that likely recognizes and cuts at the AATTAACTTAT motif in the and in the circularized version (resulting in Yucahu-i linearization) and may be involved in integration of the linear sequence...
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Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
- Robin Kosch,
- Katharina Limm,
- Annette M. Staiger,
- Nadine S. Kurz,
- Nicole Seifert,
- Bence Oláh,
- Stefan Solbrig,
- Viola Poeschel,
- Gerhard Held,
- Marita Ziepert,
- Norbert Schmitz,
- Emil Chteinberg,
- Reiner Siebert,
- Rainer Spang,
- Helena U. Zacharias,
- German Ott,
- Peter J. Oefner,
- and Michael Altenbuchinger
Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
...) is used to model common latent factors across multiple omics layers (Argelaguet et al. 2018). Unified nonnegative matrix factorization (UNMF) focuses on decomposing nonnegative matrices into interpretable, lower-dimensional components that capture the underlying structure and patterns within individual...
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Research: Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
- Matthias H. Weissensteiner,
- Andy W.C. Pang,
- Ignas Bunikis,
- Ida Höijer,
- Olga Vinnere-Petterson,
- Alexander Suh,
- and Jochen B.W. Wolf
Genome Res. May 2017 27: 697-708; Published in Advance March 30, 2017, doi:10.1101/gr.215095.116
...the OM assembly to perform hybrid scaffolding on both the SR and LR assemblies. First, the sequence assembly contigs or scaffolds were converted into sequence maps by running an “in silico digestion” based on the known Nt.BspQI recognition motif using the IrysView software (BioNano Genomics). Then...
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Research: Diversification and collapse of a telomere elongation mechanism
- Bastien Saint-Leandre,
- Son C. Nguyen,
- and Mia T. Levine
Genome Res. June 2019 29: 920-931; Published in Advance May 28, 2019, doi:10.1101/gr.245001.118
...subclade retrotransposons uncovered by our pipeline specialize at chromosome ends in their respective host species. Testing this prediction first requires molecular biology to confirm that (1) these in silico–generated consensus sequences represent actual elements in the targeted s and (2) the elements...
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Research: Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains
- Yoko Arimizu,
- Yumi Kirino,
- Mitsuhiko P. Sato,
- Koichi Uno,
- Toshio Sato,
- Yasuhiro Gotoh,
- Frédéric Auvray,
- Hubert Brugere,
- Eric Oswald,
- Jacques G. Mainil,
- Kelly S. Anklam,
- Dörte Döpfer,
- Shuji Yoshino,
- Tadasuke Ooka,
- Yasuhiro Tanizawa,
- Yasukazu Nakamura,
- Atsushi Iguchi,
- Tomoko Morita-Ishihara,
- Makoto Ohnishi,
- Koichi Akashi,
- Tetsuya Hayashi,
- and Yoshitoshi Ogura
Genome Res. September 2019 29: 1495-1505; Published in Advance August 22, 2019, doi:10.1101/gr.249268.119
...and not closely related to each other (less than five SNP distance).Assembly and annotationGenome assembly, scaffolding, and gap-closing of the Illumina sequence reads obtained in this study and from public databases were performed using the Platanus assembler (Kajitani et al. 2014). Original assemblies were used...
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Research: Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence
- Shamoni Maheshwari,
- Takayoshi Ishii,
- C. Titus Brown,
- Andreas Houben,
- and Luca Comai
Genome Res. March 2017 27: 471-478; Published in Advance February 21, 2017, doi:10.1101/gr.214619.116
...with available genomic scaffolds. In brief, we extracted CEN180 variants from all available A. thaliana genomic sequences, partitioned the variants into clusters with shared segregating sites, and then probed for sequence fingerprints of each cluster in CENH3 ChIP-seq data sets. The fact that experimental FISH...

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