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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...CNA-driven esophageal adenocarcinomas (EACs), rare SNV-driven granulosa cell tumors, and ovarian carcinoma (OVCA) with different subtypes (The Cancer Genome Atlas Research Network 2011, 2017; Nones et al. 2014; Frankell et al. 2019; Roze et al. 2020; Smith et al. 2023).ResultsMultimodal -wide cf...
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Method: Proxy panels enable privacy-aware outsourcing of genotype imputation
- Degui Zhi,
- Xiaoqian Jiang,
- and Arif Harmanci
Genome Res. February 2025 35: 326-339; Published in Advance January 10, 2025, doi:10.1101/gr.278934.124
...al. 2012) when the assumptions are not satisfied (Sampson and Zhao 2009).In the context of imputation outsourcing, the imputation server (which are sometimes referred to as the “processors”) and the data owners/controllers (query and reference data owners) must make sure to take precautions...
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Research: Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes
- Eskeatnaf Mulugeta,
- Evelyne Wassenaar,
- Esther Sleddens-Linkels,
- Wilfred F.J. van IJcken,
- Edith Heard,
- J. Anton Grootegoed,
- Walter Just,
- Joost Gribnau,
- and Willy M. Baarends
Genome Res. September 2016 26: 1202-1210; Published in Advance August 10, 2016, doi:10.1101/gr.201665.115
...Whole Genome Mapping System and processed using Genome-Builder (OpGen) as described in the Supplemental Methods. A data summary is shown in Supplemental Table S2. Quality controls, including alignment to previously sequenced E. lutescens genes, and GC and repeat content are summarized...
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LETTER: An Arabidopsis gene network based on the graphical Gaussian model
- Shisong Ma,
- Qingqiu Gong,
- and Hans J. Bohnert
Genome Res. November 2007 17: 1614-1625; Published in Advance October 5, 2007, doi:10.1101/gr.6911207
...as subnetworks and added novel components to known edges. Finally, the network reconciled individual subnetworks in a topology joined at the whole-genome level and provided a general framework that can instruct future studies on plant metabolism and stress responses. The network model is included. Footnotes...
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Methods: MAVID: Constrained Ancestral Alignment of Multiple Sequences
- Nicolas Bray and
- Lior Pachter
Genome Res. April 2004 14: 693-699; doi:10.1101/gr.1960404
..., and Rat Whole-Genome Multiple Alignment We aligned the human (April 2003), mouse (February 2003), and rat (June 2003) s using MAVID. A homology map for the s was built by C. Dewey (in prep.), and was used to generate gene anchors and constraints. Figure 3 summarizes the exon coverage of the alignment...
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Letter: BioViews: Java-Based Tools for Genomic Data Visualization
- Gregg A. Helt,
- Suzanna Lewis,
- Ann E. Loraine,
- and Gerald M. Rubin
Genome Res. March 1, 1998 8: 291-305; doi:10.1101/gr.8.3.291
..., labeling, and positioning annotations, and specifiying the annotation’s shape and color. The API also includes methods for manipulating the entire map, such as scaling and scrolling. We envision three distinct levels of reuse for the BioViews software: the whole Genome browser, the BioViews components...

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