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Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...between genetic variants and environmental stressors is key to understanding the mechanisms underlying neurological diseases. In this study, we use human brain organoids to explore how varying oxygen levels expose context-dependent gene regulatory effects. By subjecting a genetically diverse panel of 21...
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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
...at late aging stages, while genes involved in 35 myelination are downregulated at early aging stages in oligodendrocyte. Our multiomic atlas 36 underscores the substantial regulatory network changes during aging that may predispose to 37 PD, providing valuable insights for furthering understanding of PD...
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Method: Debiased personalized gene coexpression networks for population-scale scRNA-seq data
- Shan Lu and
- Sunduz Keles
Genome Res. June 9, 2023 gr.277363.122; Published in Advance June 9, 2023, doi:10.1101/gr.277363.122
...the phenotypes of interest (Lareau et al., 2015). Instead of focusing on high centrality genes within a single coexpression network, detecting genes with differential centrality between phenotypic groups can elucidate regulatory alterations. Savino et al. (2020) offer insights into the potential regulatory...
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Research: Identification of FMR1-regulated molecular networks in human neurodevelopment
- Meng Li,
- Junha Shin,
- Ryan D. Risgaard,
- Molly J. Parries,
- Jianyi Wang,
- Deborah Chasman,
- Shuang Liu,
- Sushmita Roy,
- Anita Bhattacharyya,
- and Xinyu Zhao
Genome Res. March 2020 30: 361-374; Published in Advance March 16, 2020, doi:10.1101/gr.251405.119
...–Madison, Madison, WI 53715, USA Corresponding authors: Xinyu.zhao@wisc.edu, bhattacharyy@waisman.wisc.edu, sroy@biostat.wisc.eduAbstractRNA-binding proteins (RNA-BPs) play critical roles in development and disease to regulate gene expression. However, -wide identification of their targets in primary human cells...
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Method: HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology
- Raunak Shrestha,
- Ermin Hodzic,
- Thomas Sauerwald,
- Phuong Dao,
- Kendric Wang,
- Jake Yeung,
- Shawn Anderson,
- Fabio Vandin,
- Gholamreza Haffari,
- Colin C. Collins,
- and S. Cenk Sahinalp
Genome Res. September 2017 27: 1573-1588; Published in Advance July 18, 2017, doi:10.1101/gr.221218.117
...Prioritizing molecular alterations that act as drivers of cancer remains a crucial bottleneck in therapeutic development. Here we introduce HIT’nDRIVE, a computational method that integrates genomic and transcriptomic data to identify a set of patient-specific, sequence-altered genes, with sufficient...
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Method: Linking the signaling cascades and dynamic regulatory networks controlling stress responses
- Anthony Gitter,
- Miri Carmi,
- Naama Barkai,
- and Ziv Bar-Joseph
Genome Res. February 2013 23: 365-376; Published in Advance October 11, 2012, doi:10.1101/gr.138628.112
...ratio relative to the level before sorbitol treatment. (Error bars) SD of the protein level ratios over all replicates. Gitter et al. 370 Genome Research www..org Figure 5. Knockouts affect downstream expression of genes on the recovered regulatory paths. (A) The six proteins from different regions...
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REVIEW: The Synuclein Family
- Christian Lavedan
Genome Res. September 1, 1998 8: 871-880; doi:10.1101/gr.8.9.871
...The Synuclein Family Christian Lavedan 1 Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892 USA Abstract The synuclein gene family recently came into the spotlight, when one...
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LETTER: Genomic copy number and expression variation within the C57BL/6J inbred mouse strain
- Dawn E. Watkins-Chow and
- William J. Pavan
Genome Res. January 2008 18: 60-66; Published in Advance November 21, 2007, doi:10.1101/gr.6927808
...allele frequencies in first generation (F1) progeny of C57BL/6J mice. Sequencing, quantitative PCR, breeding, and array comparative genomic hybridization (CGH) together confirmed the presence of two CNVs. Both CNVs span genes encoded on chromosome 19, and quantitative RT-PCR demonstrated that they result...
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REPORT: Generation and Comparative Analysis of ∼3.3 Mb of Mouse Genomic Sequence Orthologous to the Region of Human Chromosome 7q11.23 Implicated in Williams Syndrome
- Udaya DeSilva,
- Laura Elnitski,
- Jacquelyn R. Idol,
- Johannah L. Doyle,
- Weiniu Gan,
- James W. Thomas,
- Scott Schwartz,
- Nicole L. Dietrich,
- Stephen M. Beckstrom-Sternberg,
- Jennifer C. McDowell,
- Robert W. Blakesley,
- Gerard G. Bouffard,
- Pamela J. Thomas,
- Jeffrey W. Touchman,
- Webb Miller,
- and Eric D. Green
Genome Res. January 1, 2002 12: 3-15; doi:10.1101/gr.214802
.... The evidence that these are authentic genes includes the identification of cDNA sequences matching the mouse genomic sequence, their overlap with GenScan -predicted gene models (in all but one case), and the presence of strong mouse–human sequence conservation; these features are detailed in Figure 3...
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LETTER: Analysis of the Gene-Dense Major Histocompatibility Complex Class III Region and Its Comparison to Mouse
- Tao Xie,
- Lee Rowen,
- Begoña Aguado,
- Mary Ellen Ahearn,
- Anup Madan,
- Shizhen Qin,
- R. Duncan Campbell,
- and Leroy Hood
Genome Res. December 2003 13: 2621-2636; doi:10.1101/gr.1736803
...to numerous diseases. To facilitate understanding of this medically important and architecturally interesting portion of the genome, we have sequenced and analyzed both the human and mouse class III regions. The cross-species comparison has facilitated the identification of 60 genes in human and 61 in mouse...

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