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Method: Secure discovery of genetic relatives across large-scale and distributed genomic data sets
- Matthew M. Hong,
- David Froelicher,
- Ricky Magner,
- Victoria Popic,
- Bonnie Berger,
- and Hyunghoon Cho
Genome Res. September 2024 34: 1312-1323; Published in Advance August 7, 2024, doi:10.1101/gr.279057.124
...-Relate on the UK Biobank and All of Us data sets. On a data set of 200,000 individuals split between two parties, SF-Relate detects 97% of third-degree or closer relatives within 15 h of runtime. Our work enables secure identification of relatives across large-scale genomic data sets.Collaborative studies that aim...
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Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...BM, et al. 2025. 595 Leveraging Automated Machine Learning for Environmental DataDriven Genetic 596 Analysis and Genomic Prediction in Maize Hybrids. Advanced Science 2412423. 597 doi:10.1002/advs.202412423 598 Ibrahim AA, Ridwan RL, Muhammed MM, Abdulaziz RO, Saheed GA. 2020. Comparison of the 599...
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Method: Secure phasing of private genomes in a trusted execution environment with TX-Phase
- Natnatee Dokmai,
- Kaiyuan Zhu,
- S. Cenk Sahinalp,
- and Hyunghoon Cho
Genome Res. December 2025 35: 2626-2636; Published in Advance November 12, 2025, doi:10.1101/gr.280558.125
...in a TEE-enabled computing environment. The user verifies the enclave and submits unphased genotypes as input samples to the SP. The SP then uses TX-Phase, alongside a large reference panel of haplotype sequences (which is accessible only to the SP), to phase the genotype samples and returns the phased...
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Method: Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR
- Artem Mikelov,
- George Nefediev,
- Alexander Tashkeev,
- Oscar L. Rodriguez,
- Diego Aguilar Ortmans,
- Valeriia Skatova,
- Mark Izraelson,
- Alexey N. Davydov,
- Stanislav Poslavsky,
- Souad Rahmouni,
- Corey T. Watson,
- Dmitriy Chudakov,
- Scott D. Boyd,
- and Dmitry Bolotin
Genome Res. December 2024 34: 2293-2303; Published in Advance October 21, 2024, doi:10.1101/gr.278775.123
.... 2015. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics 31: 3356–3358. doi:10.1093/bioinformatics/btv359 ↵Hart A, Martínez S. 2023. spgs: Statistical patterns in genomic sequences. Retrieved from https...
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Research: Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing
- Sergey Aganezov,
- Sara Goodwin,
- Rachel M. Sherman,
- Fritz J. Sedlazeck,
- Gayatri Arun,
- Sonam Bhatia,
- Isac Lee,
- Melanie Kirsche,
- Robert Wappel,
- Melissa Kramer,
- Karen Kostroff,
- David L. Spector,
- Winston Timp,
- W. Richard McCombie,
- and Michael C. Schatz
Genome Res. September 2020 30: 1258-1273; Published in Advance September 4, 2020, doi:10.1101/gr.260497.119
...cancer patients using Illumina/10x Genomics, Pacific Biosciences (PacBio), and Oxford Nanopore Technologies (ONT) sequencing. We then inferred SVs and large-scale allele-specific copy number variants (CNVs) using an ensemble of methods. Our findings show that long-read sequencing allows for substantially...
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Method: Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants
- Iraad F. Bronner,
- Thomas D. Otto,
- Min Zhang,
- Kenneth Udenze,
- Chengqi Wang,
- Michael A. Quail,
- Rays H.Y. Jiang,
- John H. Adams,
- and Julian C. Rayner
Genome Res. July 2016 26: 980-989; Published in Advance May 10, 2016, doi:10.1101/gr.200279.115
...) in competitive growth conditions. Quantitation and screening of piggyBac mutants Genome Research 985 www..org to inhibitory compounds (Pradhan et al. 2015) or with the ability to survive environmental stresses such as heat shock. There are two fundamental approaches to performing such screens, either using pools...
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LETTER: A Software System for Data Analysis in Automated DNA Sequencing
- Michael C. Giddings,
- Jessica Severin,
- Michael Westphall,
- Jiazhen Wu,
- and Lloyd M. Smith
Genome Res. June 1, 1998 8: 644-665; doi:10.1101/gr.8.6.644
...-known base-calling programs for sequencing the M13mp18 vector sequence. [The sequence data described in this paper have been submitted to the GenBank data library under accession no. AF025422 ] Large-scale sequencing efforts have begun to approach the goals initially outlined for the Human Genome Project...
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Methods: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
- Bastien Chevreux,
- Thomas Pfisterer,
- Bernd Drescher,
- Albert J. Driesel,
- Werner E.G. Müller,
- Thomas Wetter,
- and Sándor Suhai
Genome Res. June 2004 14: 1147-1159; Published in Advance May 12, 2004, doi:10.1101/gr.1917404
...Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs Bastien Chevreux 1 , 7 , Thomas Pfisterer 2 , Bernd Drescher 3 , Albert J. Driesel 4 , Werner E.G. Müller 5 , Thomas...
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REVIEW: Automation for Genomics, Part One: Preparation for Sequencing
- Deirdre Meldrum
Genome Res. August 1, 2000 10: 1081-1092; doi:10.1101/gr.101400
...–96 samples by pipette or by 384 pins and output in formats from a single well to a 1536 high-density array. The HomeBase is a compact, environmentally controlled plate store for genetics samples that is custom-made to the customers' specifications. Beckman Coulter, Inc. ( http://www.beckmancoulter.com ) has...
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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
..., Amphibians and Fish, Working Group for Wildlife Research, 35392 Giessen, Germany; 8Socio-économie, Environnement et Développement (SEED), University of Liege (Arlon Campus Environment), 81001 Arlon, Belgium; 9Department of Life Sciences and Systems Biology, University of Turin, 10123 Torino, Italy; 10...

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