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Method: Interpretable phenotype decoding from multicondition sequencing data with ALPINE
- Wei-Hao Lee,
- Lechuan Li,
- Ruth Dannenfelser,
- and Vicky Yao
Genome Res. December 2025 35: 2756-2769; Published in Advance October 22, 2025, doi:10.1101/gr.280566.125
...; 4Rice Synthetic Biology Institute, Rice University, Houston, Texas 77005, USA ↵5 These authors contributed equally to this work. Corresponding author: vy@rice.eduAbstractAs sequencing techniques advance in precision, affordability, and diversity, an abundance of heterogeneous sequencing data has...
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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
...Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA; 3Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 4Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; 5...
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Research: A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia
- Haloom Rafehi,
- Liam G. Fearnley,
- Justin Read,
- Penny Snell,
- Kayli C. Davies,
- Liam Scott,
- Greta Gillies,
- Genevieve C. Thompson,
- Tess A. Field,
- Aleena Eldo,
- Simon Bodek,
- Ernest Butler,
- Luke Chen,
- John Drago,
- Himanshu Goel,
- Anna Hackett,
- G. Michael Halmagyi,
- Andrew Hannaford,
- Katya Kotschet,
- Kishore R. Kumar,
- Smitha Kumble,
- Matthew Lee-Archer,
- Abhishek Malhotra,
- Mark Paine,
- Michael Poon,
- Kate Pope,
- Katrina Reardon,
- Steven Ring,
- Anne Ronan,
- Matthew Silsby,
- Renee Smyth,
- Chloe Stutterd,
- Mathew Wallis,
- John Waterston,
- Thomas Wellings,
- Kirsty West,
- Christine Wools,
- Kathy H.C. Wu,
- David J. Szmulewicz,
- Martin B. Delatycki,
- Melanie Bahlo,
- and Paul J. Lockhart
Genome Res. April 2025 35: 769-785; Published in Advance February 27, 2025, doi:10.1101/gr.279634.124
...A prospective trial comparing programmable targeted long-read sequencing and short-read sequencing for genetic diagnosis of cerebellar ataxia Haloom Rafehi1,2,43, Liam G. Fearnley1,2,43, Justin Read3,4,43, Penny Snell3, Kayli C. Davies3,5, Liam Scott1, Greta Gillies3, Genevieve C. Thompson3,5, Tess...
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Research: Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches
- Merel Stemerdink,
- Tabea Riepe,
- Nick Zomer,
- Renee Salz,
- Michael Kwint,
- Jaap Oostrik,
- Raoul Timmermans,
- Barbara Ferrari,
- Stefano Ferrari,
- Alfredo Dueñas Rey,
- Emma Delanote,
- Suzanne E. de Bruijn,
- Hannie Kremer,
- Susanne Roosing,
- Frauke Coppieters,
- Alexander Hoischen,
- Frans P.M. Cremers,
- Peter A.C. ‘t Hoen,
- Erwin van Wijk,
- and Erik de Vrieze
Genome Res. April 2025 35: 725-739; Published in Advance March 4, 2025, doi:10.1101/gr.280060.124
...University Medical Center, Nijmegen 6525 GA, The Netherlands ↵10 These authors contributed equally to this work. Corresponding author: erik.devrieze@radboudumc.nlAbstractSequencing technologies have long limited the comprehensive investigation of large transcripts associated with inherited retinal diseases...
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Research: Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina
- Meng Wang,
- Yumei Li,
- Jun Wang,
- Soo Hwan Oh,
- Yexuan Cao,
- and Rui Chen
Genome Res. April 2025 35: 740-754; Published in Advance March 6, 2025, doi:10.1101/gr.279167.124
...Meng Wang1, Yumei Li1,2, Jun Wang1, Soo Hwan Oh1, Yexuan Cao1 and Rui Chen1,2 1Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; 2Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA Corresponding author: ruichen...
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Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
- Sena A. Gocuk,
- James Lancaster,
- Shian Su,
- Jasleen K. Jolly,
- Thomas L. Edwards,
- Doron G. Hickey,
- Matthew E. Ritchie,
- Marnie E. Blewitt,
- Lauren N. Ayton,
- and Quentin Gouil
Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
...Sena A. Gocuk1,2,3,7, James Lancaster4,7, Shian Su4,5, Jasleen K. Jolly6, Thomas L. Edwards2,3, Doron G. Hickey2, Matthew E. Ritchie4,5, Marnie E. Blewitt4,5, Lauren N. Ayton1,2,3,8 and Quentin Gouil4,5,8 1Department of Optometry and Vision Sciences, The University of Melbourne, Parkville Victoria...
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Method: Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework
- Haotian Teng,
- Marcus Stoiber,
- Ziv Bar-Joseph,
- and Carl Kingsford
Genome Res. November 2024 34: 1987-1999; Published in Advance October 15, 2024, doi:10.1101/gr.278960.124
...@cs.cmu.eduAbstractDirect nanopore-based RNA sequencing can be used to detect posttranscriptional base modifications, such as N6-methyladenosine (m6A) methylation, based on the electric current signals produced by the distinct chemical structures of modified bases. A key challenge is the scarcity of adequate training data...
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Research: Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region
- Matthew T. Maurano,
- Sitharam Ramaswami,
- Paul Zappile,
- Dacia Dimartino,
- Ludovic Boytard,
- André M. Ribeiro-dos-Santos,
- Nicholas A. Vulpescu,
- Gael Westby,
- Guomiao Shen,
- Xiaojun Feng,
- Megan S. Hogan,
- Manon Ragonnet-Cronin,
- Lily Geidelberg,
- Christian Marier,
- Peter Meyn,
- Yutong Zhang,
- John Cadley,
- Raquel Ordoñez,
- Raven Luther,
- Emily Huang,
- Emily Guzman,
- Carolina Arguelles-Grande,
- Kimon V. Argyropoulos,
- Margaret Black,
- Antonio Serrano,
- Melissa E. Call,
- Min Jae Kim,
- Brendan Belovarac,
- Tatyana Gindin,
- Andrew Lytle,
- Jared Pinnell,
- Theodore Vougiouklakis,
- John Chen,
- Lawrence H. Lin,
- Amy Rapkiewicz,
- Vanessa Raabe,
- Marie I. Samanovic,
- George Jour,
- Iman Osman,
- Maria Aguero-Rosenfeld,
- Mark J. Mulligan,
- Erik M. Volz,
- Paolo Cotzia,
- Matija Snuderl,
- and Adriana Heguy
Genome Res. December 2020 30: 1781-1788; Published in Advance October 22, 2020, doi:10.1101/gr.266676.120
....snuderl@nyulangone.org, adriana.heguy@nyulangone.orgAbstractEffective public response to a pandemic relies upon accurate measurement of the extent and dynamics of an outbreak. Viral sequencing has emerged as a powerful approach to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical...
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Method: Molecular barcoding of native RNAs using nanopore sequencing and deep learning
- Martin A. Smith,
- Tansel Ersavas,
- James M. Ferguson,
- Huanle Liu,
- Morghan C. Lucas,
- Oguzhan Begik,
- Lilly Bojarski,
- Kirston Barton,
- and Eva Maria Novoa
Genome Res. September 2020 30: 1345-1353; Published in Advance September 9, 2020, doi:10.1101/gr.260836.120
..., Mattick JS, Mercer TR. 2016. Spliced synthetic genes as internal controls in RNA sequencing experiments. Nat Methods 13: 792–798. doi:10.1038/nmeth.3958 ↵He K, Zhang X, Ren S, Sun J. 2016. Deep residual learning for image recognition. In 2016 IEEE Conference on Computer Vision and Pattern Recognition...
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Method: SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data
- Hamim Zafar,
- Nicholas Navin,
- Ken Chen,
- and Luay Nakhleh
Genome Res. November 2019 29: 1847-1859; Published in Advance October 18, 2019, doi:10.1101/gr.243121.118
...SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell sequencing data Hamim Zafar1,2, Nicholas Navin3, Ken Chen2 and Luay Nakhleh1 1Department of Computer Science, Rice University, Houston, Texas 77005, USA; 2Department of Bioinformatics...

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