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Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
...findings will be useful in guiding future studies to directly test the mechanistic predictions put forward by this meta-analysis.MethodsSelection and preparation of KCl-treated RNA sequencing data sets for analysisPublic RNA sequencing data sets of mouse primary neurons were selected for analysis...
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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
...-based proteome-wide predictions (PWPs) improve genomic prediction accuracy by an average of 3.8% compared with sequence-based PWPs. In general, predicted protein 3D structures represent a powerful approach for understanding the natural diversity of protein haplotypes.Tremendous progress has been made over...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...-Cas9 RE deletionsPaired sgRNAs (5′- and 3′-sgRNAs) were designed to target both ends of selected candidate REs in the human DNAJC9 locus to create a deletion. sgRNA with on-target high predicted cleavage and a low number of off-targets was carefully selected using the UCSC Genome Browser (hg38) (Perez...
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Research: Meta-analysis of human and mouse ALS astrocytes reveals multi-omic signatures of inflammatory reactive states
- Oliver J. Ziff,
- Benjamin E. Clarke,
- Doaa M. Taha,
- Hamish Crerar,
- Nicholas M. Luscombe,
- and Rickie Patani
Genome Res. January 2022 32: 71-84; Published in Advance December 28, 2021, doi:10.1101/gr.275939.121
...://shiny.crick.ac.uk/ALS_reactive_astrocytes_meta/.View larger version: In this window In a new window Figure 2. Meta-analysis of ALS hiPSC-astrocytes and correlation with A1 astrocytes. (A) Schematic depicting hiPSC-astrocyte differentiation in ALS mutant astrocytes (VCP, yellow; SOD1, blue; C9orf72, green; FUS, purple) and A1 hiPSC-astrocytes from five...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...contributed equally to this work. Corresponding authors: thomas.near@yale.edu, clad@ihb.ac.cn, yangliandong1987@163.comAbstractGenomic evolution can propel and restrict species diversification. Rapid molecular evolution and genomic rearrangement is often associated with increased species diversification...
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Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...Bafna1,4 1Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA; 2Bionano Genomics, Incorporated, San Diego, California 92121, USA; 3Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, 1090...
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Research: Optical genome mapping enables accurate testing of large repeat expansions
- Bart van der Sanden,
- Kornelia Neveling,
- Syukri Shukor,
- Michael D. Gallagher,
- Joyce Lee,
- Stephanie L. Burke,
- Maartje Pennings,
- Ronald van Beek,
- Michiel Oorsprong,
- Ellen Kater-Baats,
- Eveline Kamping,
- Alide A. Tieleman,
- Nicol C. Voermans,
- Ingrid E. Scheffer,
- Jozef Gecz,
- Mark A. Corbett,
- Lisenka E.L.M. Vissers,
- Andy Wing Chun Pang,
- Alex Hastie,
- Erik-Jan Kamsteeg,
- and Alexander Hoischen
Genome Res. April 2025 35: 810-823; Published in Advance March 20, 2025, doi:10.1101/gr.279491.124
...whether a sample contains evidence for somatic instability or not.DiscussionDetermining the exact length of specific repeat expansions is of great importance for the patient and their family due to the rough correlation between repeat size and disease severity and age of onset, but also due to genetic...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...comprehensive genomic and epigenomic profiles of patients. Instances of ultrarapid sequencing in critical care settings have demonstrated the effectiveness of same-day LRS workflows for clinical genetics, as shown by Gorzynski et al. (2022) and Goenka et al. (2022).LRS technologies have now reached levels...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...: chirag@iisc.ac.inAbstractAffordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single-nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference is unreliable in highly polymorphic...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...1 assembly. Independently, we predicted 23,249 genomic loci encoding StringTie2 transcripts assembled from ribodepleted RNA-seq data (Wang et al. 2022). These transcripts overlapped with (and thus confirmed) known or predicted N2 or AUGUSTUS protein-coding genes and with known N2 ncRNA genes (Table...
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