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Research: Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing
- Jesper Eisfeldt,
- Edward J. Higginbotham,
- Felix Lenner,
- Jennifer Howe,
- Bridget A. Fernandez,
- Anna Lindstrand,
- Stephen W. Scherer,
- and Lars Feuk
Genome Res. November 2024 34: 1763-1773; Published in Advance October 29, 2024, doi:10.1101/gr.279263.124
...Resolving complex duplication variants in autism spectrum disorder using long-read sequencing Jesper Eisfeldt1,2, Edward J. Higginbotham3,4, Felix Lenner5, Jennifer Howe3,4, Bridget A. Fernandez6,7, Anna Lindstrand1,2, Stephen W. Scherer3,4,8 and Lars Feuk5 1Department of Molecular Medicine...
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Resource: The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
- Simon Bray,
- John Chilton,
- Matthias Bernt,
- Nicola Soranzo,
- Marius van den Beek,
- Bérénice Batut,
- Helena Rasche,
- Martin Čech,
- Peter J.A. Cock,
- Björn Grüning,
- and Anton Nekrutenko
Genome Res. February 2023 33: 261-268; Published in Advance February 24, 2023, doi:10.1101/gr.276963.122
...and command-line application that is used extensively as a software development kit by Galaxy or Common Workflow Language (CWL) ( Crusoe et al. 2022 ) tool, workflow, and training material developers, as well as a toolkit for Galaxy “power users.” Planemo provides a simple but powerful command-line interface...
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Method: Resolving the chromatin impact of mosaic variants with targeted Fiber-seq
- Stephanie C. Bohaczuk,
- Zachary J. Amador,
- Chang Li,
- Benjamin J. Mallory,
- Elliott G. Swanson,
- Jane Ranchalis,
- Mitchell R. Vollger,
- Katherine M. Munson,
- Tom Walsh,
- Morgan O. Hamm,
- Yizi Mao,
- Andre Lieber,
- and Andrew B. Stergachis
Genome Res. December 2024 34: 2269-2278; Published in Advance December 9, 2024, doi:10.1101/gr.279747.124
...of an internal nucleosome varied across the individual reads (Fig. 1F), indicating that the precise pattern of accessibility within a promoter can vary quite substantially from fiber to fiber.Given the potential for targeted Fiber-seq to synchronously resolve alterations in both the and chromatin epi at single...
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Method: An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride
- Inswasti Cahyani,
- John Tyson,
- Nadine Holmes,
- Josh Quick,
- Chris Moore,
- Nick Loman,
- and Matthew Loose
Genome Res. May 2025 35: 1154-1166; Published in Advance March 24, 2025, doi:10.1101/gr.279943.124
...interplay of DNA quality, library preparation, read length, and yield, we tested a range of UL protocols aimed at maximizing both read length and yield (Fig. 1B).View larger version: In this window In a new window Figure 1. Summary of the FindingNemo toolkit. (A) Similarities and differences between...
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Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
- Christine E. Schnitzler,
- E. Sally Chang,
- Justin Waletich,
- Gonzalo Quiroga-Artigas,
- Wai Yee Wong,
- Anh-Dao Nguyen,
- Sofia N. Barreira,
- Liam B. Doonan,
- Paul Gonzalez,
- Sergey Koren,
- James M. Gahan,
- Steven M. Sanders,
- Brian Bradshaw,
- Timothy Q. DuBuc,
- Febrimarsa,
- Danielle de Jong,
- Eric P. Nawrocki,
- Alexandra Larson,
- Samantha Klasfeld,
- Sebastian G. Gornik,
- R. Travis Moreland,
- Tyra G. Wolfsberg,
- Adam M. Phillippy,
- James C. Mullikin,
- Oleg Simakov,
- Paulyn Cartwright,
- Matthew Nicotra,
- Uri Frank,
- and Andreas D. Baxevanis
Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
...The of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals Christine E. Schnitzler1,2, E. Sally Chang3,4, Justin Waletich1,2, Gonzalo Quiroga-Artigas1,2,5, Wai Yee Wong6, Anh-Dao Nguyen3, Sofia N. Barreira3, Liam B. Doonan7...
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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
...Assembly of a pan for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history Yang Zhou1,6, Lv Yang1,6, Xiaotao Han1, Jiazheng Han1, Yan Hu1, Fan Li1, Han Xia1, Lingwei Peng1, Clarissa Boschiero2, Benjamin D...
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Method: Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
- Ian T. Fiddes,
- Joel Armstrong,
- Mark Diekhans,
- Stefanie Nachtweide,
- Zev N. Kronenberg,
- Jason G. Underwood,
- David Gordon,
- Dent Earl,
- Thomas Keane,
- Evan E. Eichler,
- David Haussler,
- Mario Stanke,
- and Benedict Paten
Genome Res. July 2018 28: 1029-1038; Published in Advance June 8, 2018, doi:10.1101/gr.233460.117
...Comparative Annotation Toolkit (CAT)—simultaneous clade and personal annotation Ian T. Fiddes1,2, Joel Armstrong1,8, Mark Diekhans1,8, Stefanie Nachtweide3,8, Zev N. Kronenberg4, Jason G. Underwood4,5, David Gordon4,6, Dent Earl1, Thomas Keane7, Evan E. Eichler4,6, David Haussler1, Mario Stanke3...
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Method: Resolving the full spectrum of human genome variation using Linked-Reads
- Patrick Marks,
- Sarah Garcia,
- Alvaro Martinez Barrio,
- Kamila Belhocine,
- Jorge Bernate,
- Rajiv Bharadwaj,
- Keith Bjornson,
- Claudia Catalanotti,
- Josh Delaney,
- Adrian Fehr,
- Ian T. Fiddes,
- Brendan Galvin,
- Haynes Heaton,
- Jill Herschleb,
- Christopher Hindson,
- Esty Holt,
- Cassandra B. Jabara,
- Susanna Jett,
- Nikka Keivanfar,
- Sofia Kyriazopoulou-Panagiotopoulou,
- Monkol Lek,
- Bill Lin,
- Adam Lowe,
- Shazia Mahamdallie,
- Shamoni Maheshwari,
- Tony Makarewicz,
- Jamie Marshall,
- Francesca Meschi,
- Christopher J. O'Keefe,
- Heather Ordonez,
- Pranav Patel,
- Andrew Price,
- Ariel Royall,
- Elise Ruark,
- Sheila Seal,
- Michael Schnall-Levin,
- Preyas Shah,
- David Stafford,
- Stephen Williams,
- Indira Wu,
- Andrew Wei Xu,
- Nazneen Rahman,
- Daniel MacArthur,
- and Deanna M. Church
Genome Res. April 2019 29: 635-645; Published in Advance March 20, 2019, doi:10.1101/gr.234443.118
..., and reduced performance in small indel calling, although this largely occurs in homopolymer regions and LCRs. Recent work suggests ambiguity in such regions may be tolerated for a large number of applications (Li et al. 2018). Although Linked-Reads can resolve many repetitive elements and regions, highly...
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Research: Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)
- Gang Li,
- Brian W. Davis,
- Eduardo Eizirik,
- and William J. Murphy
Genome Res. January 2016 26: 1-11; Published in Advance October 30, 2015, doi:10.1101/gr.186668.114
...Phylogenomic evidence for ancient hybridization in the s of living cats (Felidae) Gang Li,1 Brian W. Davis,1,2,4 Eduardo Eizirik,3 and William J. Murphy1,2 1Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA; 2Interdisciplinary Program...
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Research: Reconstructing genetic history of Siberian and Northeastern European populations
- Emily H.M. Wong,
- Andrey Khrunin,
- Larissa Nichols,
- Dmitry Pushkarev,
- Denis Khokhrin,
- Dmitry Verbenko,
- Oleg Evgrafov,
- James Knowles,
- John Novembre,
- Svetlana Limborska,
- and Anton Valouev
Genome Res. January 2017 27: 1-14; Published in Advance December 13, 2016, doi:10.1101/gr.202945.115
...and linguistically diverse indigenous ethnic groups, yet genetic variation and histories of peoples from this region are largely uncharacterized. We present deep whole- sequencing data (∼38×) from 28 individuals belonging to 14 distinct indigenous populations from that region. We combined these data sets...

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