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Research: High-throughput functional testing of ENCODE segmentation predictions
- Jamie C. Kwasnieski,
- Christopher Fiore,
- Hemangi G. Chaudhari,
- and Barak A. Cohen
Genome Res. October 2014 24: 1595-1602; Published in Advance July 17, 2014, doi:10.1101/gr.173518.114
...for their manuscript comments. This work was supported by a grant from the National Institutes of Health (R01 GM092910). References Akaike H. 1974. A new look at the statisticalmodel identification. IEEE Trans Automat Contr 19: 716–723. Arvey A, Agius P, Noble WS, Leslie C. 2012. Sequence and chromatin determinants...
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Research: High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome
- Houssam Hajjoul,
- Julien Mathon,
- Hubert Ranchon,
- Isabelle Goiffon,
- Julien Mozziconacci,
- Benjamin Albert,
- Pascal Carrivain,
- Jean-Marc Victor,
- Olivier Gadal,
- Kerstin Bystricky,
- and Aurélien Bancaud
Genome Res. November 2013 23: 1829-1838; Published in Advance September 27, 2013, doi:10.1101/gr.157008.113
...are accurately described by the Rouse model. The Rouse dynamics imply that chromosome segments search for target sites by compact exploration (de Gennes 1982), meaning that they systematically visit neighboring sites as they look for targets during repair or transcription activation (Condamin et al. 2007...
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RESOURCE: High-Throughput Computational and Experimental Techniques in Structural Genomics
- Mark R. Chance,
- Andras Fiser,
- Andrej Sali,
- Ursula Pieper,
- Narayanan Eswar,
- Guiping Xu,
- J. Eduardo Fajardo,
- Thirumuruhan Radhakannan,
- and Nebojsa Marinkovic
Genome Res. October 15, 2004 14: 2145-2154; doi:10.1101/gr.2537904
...a valuable resource for biologists worldwide. Although this sequence coverage and the number of modeled proteins may look impressive, usually only one domain within the ORF sequence of each protein is modeled. On average, proteins have two or three domains. That is, an average yeast ORFs codes for 472 amino...
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RESOURCE: Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae
- Yanhui Hu,
- Andreas Rolfs,
- Bhupinder Bhullar,
- Tellamraju V. S. Murthy,
- Cong Zhu,
- Michael F. Berger,
- Anamaria A. Camargo,
- Fontina Kelley,
- Seamus McCarron,
- Daniel Jepson,
- Aaron Richardson,
- Jacob Raphael,
- Donna Moreira,
- Elena Taycher,
- Dongmei Zuo,
- Stephanie Mohr,
- Michael F. Kane,
- Janice Williamson,
- Andrew Simpson,
- Martha L. Bulyk,
- Edward Harlow,
- Gerald Marsischky,
- Richard D. Kolodner,
- and Joshua LaBaer
Genome Res. April 2007 17: 536-543; Published in Advance February 23, 2007, doi:10.1101/gr.6037607
...: 127 – 138 . ↵ Marsischky, G. , LaBaer, J. ( 2004 ) Many paths to many clones: A comparative look at high-throughput cloning methods . Genome Res. 14 : 2020 – 2028 . ↵ Mewes, H. , Frishman, D. , Guldener, U. , Mannhaupt, G. , Mayer, K. , Mokrejs, M. , Morgenstern, B. , Munsterkotter, M. , Rudd, S...
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PERSPECTIVE: ORFeome Cloning and Systems Biology: Standardized Mass Production of the Parts From the Parts-List
- Michael A. Brasch,
- James L. Hartley,
- and Marc Vidal
Genome Res. October 15, 2004 14: 2001-2009; doi:10.1101/gr.2769804
...in the collection to any ORF in the second collection. This feature of Gateway is unique among RC systems and allows optimal compatibility in projects that require the high-throughput cloning of two or more DNA sequences in many different vectors. The Example of C. elegans The C. elegans interactome project...
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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
..., and the released DNA can be sequenced to identify all DNA sequences bound to the protein of interest using high-throughput platforms (Park 2009). Standard controls include comparing this immunoprecipitation to DNA binding by nonimmunized IgG raised in the same species as the protein targeting antibody, using q...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...switch (Fig. 1D; Supplemental Figs. S16–S18), indicating specific switching between weakly heterochromatic and euchromatic states. A further characterization of paths of subcompartment switching across the three stages shows that, fourth, a similar fraction of 24%–26% of subcompartments ends up in either...
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Method: Integrating SNVs and CNAs on a phylogenetic tree from single-cell DNA sequencing data
- Liting Zhang,
- Hank W. Bass,
- Jerome Irianto,
- and Xian Mallory
Genome Res. November 2023 33: 2002-2017; Published in Advance November 22, 2023, doi:10.1101/gr.277249.122
....7 for all cases except when tree leaf number was eight compared with SCsnvcna, whose pairwise SNV error was less than 0.15 for a majority of cases. We further looked into RobustClone's intermediate result and found that RobustClone did not place a large number of SNVs on the tree, whereas these SNVs had...
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Research: Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain
- James L. Shepherdson,
- David M. Granas,
- Jie Li,
- Zara Shariff,
- Stephen P. Plassmeyer,
- Alex S. Holehouse,
- Michael A. White,
- and Barak A. Cohen
Genome Res. October 2024 34: 1540-1552; Published in Advance September 25, 2024, doi:10.1101/gr.279415.124
...to benchmark the classification performance of the DMS assay. Although the variant classifiers in clinical use typically aggregate multiple evidence sources (including evolutionary conservation, modeling, and functional data), looking at the classification performance of this single functional assay can give...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...). They overlap with each other at the same junction, with smaller unit 842l having an overhang. Thus, there was only one possible path through it. This junction is near the collapsed duplication, suggesting a cause for the collapse. Although the unitig graph of the targeted assembly had more unitigs, the path...
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