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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
...distinct cellular states from an otherwise homogeneous . The mammalian brain consists of thousands of distinct neuronal subtypes that respond to neuronal activity through regulation of the transcriptome and proteome (Lake et al. 2016; Van Oostrum et al. 2023). Consequently, disruption of alternative...
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Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
- Irene Mei,
- Susanne Nichterwitz,
- Melanie Leboeuf,
- Jik Nijssen,
- Isadora Lenoel,
- Dirk Repsilber,
- Christian S. Lobsiger,
- and Eva Hedlund
Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
...upregulate both detrimental and regenerative responses to ALS and share pathway activation, indicating that breakdown occurs through similar mechanisms across vulnerable neurons, albeit with distinct timing. Meta-analysis across four rodent mutant Sod1 MN transcriptome data sets identify a shared...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...to high dimensionality, batch effects, dropout, and transcriptional noise (Lopez et al. 2018); therefore, scRNA-seq data analysis methods must address the inherent variability and noise in these data. This is especially important when evaluating cell states and programs through gene signature scoring...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...by DNA sequencing (ChIP-seq) of an ever growing number of TFs in different cell types, species, and conditions are revealing repeat-associated binding sites (RABS) whereby reproducible TF-DNA interactions fall within subtypes of major repeat families (Bourque et al. 2008). Coincident with their discovery...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...alterations that accompany 50 normal aging-including mitochondrial dysfunction, chronic inflammatory activation, and oxidative 51 stress-mirror key pathological processes observed in PD(Hindle 2010; Reeve et al. 2014; Collier 52 et al. 2017). In addition, genetic susceptibility and environmental exposures...
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Resource: A time-resolved multi-omic atlas of the developing mouse liver
- Tongqing Gong,
- Chunchao Zhang,
- Xiaotian Ni,
- Xianju Li,
- Jin'e Li,
- Mingwei Liu,
- Dongdong Zhan,
- Xia Xia,
- Lei Song,
- Quan Zhou,
- Chen Ding,
- Jun Qin,
- and Yi Wang
Genome Res. February 2020 30: 263-275; Published in Advance February 12, 2020, doi:10.1101/gr.253328.119
...developmentWe conducted a temporal, in-depth multi-omics analysis on mouse liver tissues collected at 15 time points from embryonic day 12.5 (E12.5, the earliest date that fetal liver is visible when the resection is possible) to postnatal week 8 (W8) (Fig. 1A). The sampling time window covers the embryonic...
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Research: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
- Peter Orchard,
- Nandini Manickam,
- Christa Ventresca,
- Swarooparani Vadlamudi,
- Arushi Varshney,
- Vivek Rai,
- Jeremy Kaplan,
- Claudia Lalancette,
- Karen L. Mohlke,
- Katherine Gallagher,
- Charles F. Burant,
- and Stephen C.J. Parker
Genome Res. December 2021 31: 2258-2275; Published in Advance November 23, 2021, doi:10.1101/gr.268482.120
...multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 33...
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Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...by acute exercise based on 18 cohorts (Amar et al. 2021). We found over one third of the genes identified as regulated in our pseudobulk DEG analysis were reported in the meta-analysis as well (Supplemental Fig. S7). To provide a comparison, we performed a similar analysis of data from a published study...
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Research: Diploid genome architecture revealed by multi-omic data of hybrid mice
- Zhijun Han,
- Kairong Cui,
- Katarzyna Placek,
- Ni Hong,
- Chengqi Lin,
- Wei Chen,
- Keji Zhao,
- and Wenfei Jin
Genome Res. August 2020 30: 1097-1106; Published in Advance August 5, 2020, doi:10.1101/gr.257568.119
...Diploid architecture revealed by multi-omic data of hybrid mice Zhijun Han1,2, Kairong Cui3, Katarzyna Placek3, Ni Hong1, Chengqi Lin2, Wei Chen1, Keji Zhao3 and Wenfei Jin1 1Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; 2Institute of Life...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...(Fig. 5A–G; Supplemental Fig. S10). Sequence analysis revealed a robust alternative start codon within the LTR7 sequence, altering the N-terminus of isoform 2 (Supplemental Fig. S11A), which was validated by mass spectrometry following overexpression (Fig. 5H; Supplemental Fig. S11B; Huang et al. 2024...
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