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Perspective: Why community consultation matters in genomic research benefit-sharing models
- Sarah LeBaron von Baeyer,
- Rebecca Crocker,
- Rindra Rakotoarivony,
- Jean Freddy Ranaivoarisoa,
- Germain Jules Spiral,
- Stephane Castel,
- Andrew Farnum,
- Holly Vance,
- Noah Collins,
- Keolu Fox,
- and Kaja Wasik
Genome Res. January 2024 34: 1-6; Published in Advance January 31, 2024, doi:10.1101/gr.278308.123
...in human genomic research, established precedents across the private and public spheres are lacking. Moreover, the few existing models for benefit sharing with populations that participate in genomic research are largely limited to intangible or nonfinancial benefits, or to top-down initiatives...
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Method: Enabling tradeoffs in privacy and utility in genomic data Beacons and summary statistics
- Rajagopal Venkatesaramani,
- Zhiyu Wan,
- Bradley A. Malin,
- and Yevgeniy Vorobeychik
Genome Res. July 2023 33: 1113-1123; Published in Advance May 22, 2023, doi:10.1101/gr.277674.123
...available by the 2016 iDASH workshop on privacy and security (Tang et al. 2016). The data consist of s of 400 individuals for whom summary statistics are to be released (i.e., the set D), and 400 individuals who are not part of this group (the set ). This data set was derived from the 1000 Genomes Project...
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Research: The genomic basis of evolutionary differentiation among honey bees
- Bertrand Fouks,
- Philipp Brand,
- Hung N. Nguyen,
- Jacob Herman,
- Francisco Camara,
- Daniel Ence,
- Darren E. Hagen,
- Katharina J. Hoff,
- Stefanie Nachweide,
- Lars Romoth,
- Kimberly K.O. Walden,
- Roderic Guigo,
- Mario Stanke,
- Giuseppe Narzisi,
- Mark Yandell,
- Hugh M. Robertson,
- Nikolaus Koeniger,
- Panuwan Chantawannakul,
- Michael C. Schatz,
- Kim C. Worley,
- Gene E. Robinson,
- Christine G. Elsik,
- and Olav Rueppell
Genome Res. July 2021 31: 1203-1215; Published in Advance May 4, 2021, doi:10.1101/gr.272310.120
...Barcelona, Spain; 14New York Genome Center, New York, New York 10013, USA; 15Utah Center for Genetic Discovery, University of Utah, Salt Lake City, Utah 84112, USA; 16Department of Behavioral Physiology and Sociobiology (Zoology II), University of Würzburg, 97074 Würzburg, Germany; 17Environmental Science...
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Resource: Instrumenting the health care enterprise for discovery research in the genomic era
- Shawn Murphy,
- Susanne Churchill,
- Lynn Bry,
- Henry Chueh,
- Scott Weiss,
- Ross Lazarus,
- Qing Zeng,
- Anil Dubey,
- Vivian Gainer,
- Michael Mendis,
- John Glaser,
- and Isaac Kohane
Genome Res. September 2009 19: 1675-1681; Published in Advance July 14, 2009, doi:10.1101/gr.094615.109
...and identified a gold-standard set of RA patients and non-RA patients (102 definite RA cases and 398 non-RA patients). Costs for large-scale i2b2 association studies We initially opted to collaborate with the physicians in the largest outpatient clinics to recruit and consent their patients as they appeared...
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Research: Genomic analysis of the causative agents of coccidiosis in domestic chickens
- Adam J. Reid,
- Damer P. Blake,
- Hifzur R. Ansari,
- Karen Billington,
- Hilary P. Browne,
- Josephine Bryant,
- Matt Dunn,
- Stacy S. Hung,
- Fumiya Kawahara,
- Diego Miranda-Saavedra,
- Tareq B. Malas,
- Tobias Mourier,
- Hardeep Naghra,
- Mridul Nair,
- Thomas D. Otto,
- Neil D. Rawlings,
- Pierre Rivailler,
- Alejandro Sanchez-Flores,
- Mandy Sanders,
- Chandra Subramaniam,
- Yea-Ling Tay,
- Yong Woo,
- Xikun Wu,
- Bart Barrell,
- Paul H. Dear,
- Christian Doerig,
- Arthur Gruber,
- Alasdair C. Ivens,
- John Parkinson,
- Marie-Adèle Rajandream,
- Martin W. Shirley,
- Kiew-Lian Wan,
- Matthew Berriman,
- Fiona M. Tomley,
- and Arnab Pain
Genome Res. October 2014 24: 1676-1685; Published in Advance July 11, 2014, doi:10.1101/gr.168955.113
...is annotated with repeat-poor (blue) and repeat-rich (red) regions $30 kb. This highlights the barcode-like patterning across the whole of each . Reid et al. 1678 Genome Research www..org Metabolism is well conserved between Eimeria and Toxoplasma (Supplemental Fig. S4; Supplemental Data set S3...
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Research: Genomic characterization of the Bacillus cereus sensu lato species: Backdrop to the evolution of Bacillus anthracis
- Michael E. Zwick,
- Sandeep J. Joseph,
- Xavier Didelot,
- Peter E. Chen,
- Kimberly A. Bishop-Lilly,
- Andrew C. Stewart,
- Kristin Willner,
- Nichole Nolan,
- Shannon Lentz,
- Maureen K. Thomason,
- Shanmuga Sozhamannan,
- Alfred J. Mateczun,
- Lei Du,
- and Timothy D. Read
Genome Res. August 2012 22: 1512-1524; Published in Advance May 29, 2012, doi:10.1101/gr.134437.111
...in any clade. We found no evidence of recent large-scale gene loss in B. anthracis or for unusual accumulation of nonsynonymous DNA substitutions in the chromosome; however, several B. cereus genomes isolated from soil and not previously associated with human disease were degraded to various degrees...
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Method: Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases
- Prashant S. Emani,
- Maya N. Geradi,
- Gamze Gürsoy,
- Monica R. Grasty,
- Andrew Miranker,
- and Mark B. Gerstein
Genome Res. December 2023 33: 2156-2173; Published in Advance December 14, 2023, doi:10.1101/gr.278322.123
...rare ones) to identify individuals has been repeatedly shown, the availability of small sets of noisy genotypes, from environmental DNA samples or functional genomics data, motivated us to quantify their informativeness. We present a computational tool suite, termed Privacy Leakage by Inference across...
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Research: Genotype imputation from low-coverage data for medical and population genetic analyses
- Simone Andrea Biagini,
- Sara Becelaere,
- Mio Aerden,
- Tatjana Jatsenko,
- Laurens Hannes,
- Philip Van Damme,
- Jeroen Breckpot,
- Koenraad Devriendt,
- Bernard Thienpont,
- Joris Robert Vermeesch,
- Isabelle Cleynen,
- and Toomas Kivisild
Genome Res. September 2025 35: 1929-1941; Published in Advance July 22, 2025, doi:10.1101/gr.280175.124
...metadata obtained at a later stage of the study, we found that our results with IBIS matched more than 90% of the recorded information related to duplicates and relatives.GDI validationWe compared the performance of QUILT across different postimputation statistics on the three test samples with high...
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Research: Major impacts of widespread structural variation on sorghum
- Zhihai Zhang,
- Joao Paulo Gomes Viana,
- Bosen Zhang,
- Kimberly K.O. Walden,
- Hans Müller Paul,
- Stephen P. Moose,
- Geoffrey P. Morris,
- Chris Daum,
- Kerrie W. Barry,
- Nadia Shakoor,
- and Matthew E. Hudson
Genome Res. February 2024 34: 286-299; Published in Advance March 13, 2024, doi:10.1101/gr.278396.123
...of DEG counts between “impact_MODERATE” and “impact_LOW” varied depending on lines and stages. In general, higher impact SVs associated more DEGs.DiscussionRecent studies have revealed an abundance of large-scale genomic variants in many plant species, but the effects of SV on global variation...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...number alterations, and some structural variants (SVs) (Choo et al. 2023). This high-throughput, cost-effective technology has facilitated large-scale cancer genomics projects like The Cancer Genome Atlas (TCGA) (The Cancer Genome Atlas Research Network et al. 2013), the International Cancer Genome...
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