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Research: Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma
- Winnie S. Liang,
- William Hendricks,
- Jeffrey Kiefer,
- Jessica Schmidt,
- Shobana Sekar,
- John Carpten,
- David W. Craig,
- Jonathan Adkins,
- Lori Cuyugan,
- Zarko Manojlovic,
- Rebecca F. Halperin,
- Adrienne Helland,
- Sara Nasser,
- Christophe Legendre,
- Laurence H. Hurley,
- Karthigayini Sivaprakasam,
- Douglas B. Johnson,
- Holly Crandall,
- Klaus J. Busam,
- Victoria Zismann,
- Valerie Deluca,
- Jeeyun Lee,
- Aleksandar Sekulic,
- Charlotte E. Ariyan,
- Jeffrey Sosman,
- and Jeffrey Trent
Genome Res. April 2017 27: 524-532; doi:10.1101/gr.213348.116
...Douglas B. Johnson,4 Holly Crandall,4 Klaus J. Busam,5 Victoria Zismann,1 Valerie Deluca,1 Jeeyun Lee,6 Aleksandar Sekulic,1,2 Charlotte E. Ariyan,5,8 Jeffrey Sosman,7,8 and Jeffrey Trent1,8 1Translational Genomics Research Institute, Phoenix, Arizona 85004, USA; 2Mayo Clinic, Scottsdale, Arizona 85259...
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Research: Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver
- Xia Yang,
- Bin Zhang,
- Cliona Molony,
- Eugene Chudin,
- Ke Hao,
- Jun Zhu,
- Andrea Gaedigk,
- Christine Suver,
- Hua Zhong,
- J. Steven Leeder,
- F. Peter Guengerich,
- Stephen C. Strom,
- Erin Schuetz,
- Thomas H. Rushmore,
- Roger G. Ulrich,
- J. Greg Slatter,
- Eric E. Schadt,
- Andrew Kasarskis,
- and Pek Yee Lum
Genome Res. August 2010 20: 1020-1036; Published in Advance June 10, 2010, doi:10.1101/gr.103341.109
...Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver Xia Yang 1 , 9 , 10 , 13 , Bin Zhang 1 , 9 , 10 , Cliona Molony 1 , Eugene Chudin 1 , Ke Hao 1 , Jun Zhu 1 , 10 , Andrea...
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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
.... These collaborative efforts have yielded invaluable insights into the molecular mechanisms underlying cancer initiation, progression, and metastasis, uncovering recurring patterns of genomic alterations, novel cancer genes, and pathways. Consequently, short-read sequencing for both tumor and germline is routinely...
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Method: Genealogy-based trait association with LOCATER boosts power at loci with allelic heterogeneity
- Xinxin Wang,
- Ryan Christ,
- Erica Young,
- Chul Joo Kang,
- Indraniel Das,
- Edward A. Belter, Jr.,
- Markku Laakso,
- Louis J.M. Aslett,
- David Steinsaltz,
- Nathan O. Stitziel,
- and Ira M. Hall
Genome Res. April 16, 2026 ; Published in Advance April 16, 2026, doi:10.1101/gr.280372.124
..., Washington University School of Medicine, Saint Louis, Missouri 63110, USA; 5McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, Missouri 63108, USA; 6Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio FI-70211, Finland; 7Department...
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Method: A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma
- Jan Müller,
- Christina Hartwig,
- Mirko Sonntag,
- Lisa Bitzer,
- Christopher Adelmann,
- Yevhen Vainshtein,
- Karolina Glanz,
- Sebastian O. Decker,
- Thorsten Brenner,
- Georg F. Weber,
- Arndt von Haeseler,
- and Kai Sohn
Genome Res. August 2024 34: 1185-1195; Published in Advance September 13, 2024, doi:10.1101/gr.279326.124
...DNA”) accumulate at open chromatin as well as gene regulatory elements. Differential enrichment of short cfDNA at genomic loci facilitated discrimination of colorectal and pancreatic cancer patient samples as well as between septic patients and clinical controls, showing potential for diagnostic applications...
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Method: Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
- Samuel T. Horsfield,
- Basil C.T. Fok,
- Yuhan Fu,
- Paul Turner,
- John A. Lees,
- and Nicholas J. Croucher
Genome Res. April 2025 35: 1025-1040; Published in Advance March 4, 2025, doi:10.1101/gr.279435.124
...Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom; 3Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX3 7LG, United Kingdom ↵4 These authors contributed equally to this work. Corresponding author: shorsfield...
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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...biomarkers for future tissue-of-origin studies.Taken together, many methylomic and fragmentomic features of cfDNA molecules have recently come into the spotlight, promising to expand our knowledge of cfDNA biology and their clinical applications. Advancements in analytical and bioinformatic tools based...
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Method: Cancer driver topologically associated domains identify oncogenic and tumor-suppressive lncRNAs
- Ziyan Rao,
- Min Zhang,
- Shaodong Huang,
- Chenyang Wu,
- Yuheng Zhou,
- Weijie Zhang,
- Xia Lin,
- and Dongyu Zhao
Genome Res. August 2025 35: 1842-1858; Published in Advance May 27, 2025, doi:10.1101/gr.280235.124
...aspects of cancer lncRNAs, including their expression patterns, genomic locations, and direct interactions with cancer driver PCGs, and developed a pipeline to identify candidate cancer driver lncRNAs. Finally, we validate the reliability of potential cancer driver lncRNAs through functional analysis...
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Mini-Review: Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
- William J. Murphy and
- Andrew J. Harris
Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123
...functional and population genomic studies are needed to further understand the impact of X Chromosome structural variation on reproductive isolation and trait evolution across the mammalian tree of life.A path toward T2T s for all catsThe domestic cat has been among the most well-developed mammalian...
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Method: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information
- Zhoutao Chen,
- Long Pham,
- Tsai-Chin Wu,
- Guoya Mo,
- Yu Xia,
- Peter L. Chang,
- Devin Porter,
- Tan Phan,
- Huu Che,
- Hao Tran,
- Vikas Bansal,
- Justin Shaffer,
- Pedro Belda-Ferre,
- Greg Humphrey,
- Rob Knight,
- Pavel Pevzner,
- Son Pham,
- Yong Wang,
- and Ming Lei
Genome Res. June 2020 30: 898-909; Published in Advance June 15, 2020, doi:10.1101/gr.260380.119
.... 2019) showed the most promising results to bring routine long-read capability to second-generation platforms. The general concept underlining these clonal-barcoding technologies is to uniquely label subfragments of a long genomic DNA fragment with a common barcode sequence when breaking the long...

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