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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V. Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...in bulk tumor samples. However, it is currently unclear how the difference in expression levels between tumor and normal cells affects the assessment of somatic mutant allele expression relative to its VAFDNA. Tumor and normal tissues are known to exhibit differential gene expressions (Zhang et al. 1997...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
..., or PASs on an mRNA have all historically been thought to occur independently, increasing evidence suggests extensive coordination to regulate the expression of full-length isoforms (Alfonso-Gonzalez and Hilgers 2024). For instance, recent studies have identified coupling between alternative TSSs...
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Resource: Genome-scale targeted mutagenesis in Brassica napus using a pooled CRISPR library
- Jianjie He,
- Kai Zhang,
- Shuxiang Yan,
- Mi Tang,
- Weixian Zhou,
- Yongtai Yin,
- Kang Chen,
- Chunyu Zhang,
- and Maoteng Li
Genome Res. May 2023 33: 798-809; Published in Advance June 8, 2023, doi:10.1101/gr.277650.123
...@mail.hzau.edu.cn, limaoteng426@hust.edu.cnAbstractThe recently constructed mutant libraries of diploid crops by the CRISPR-Cas9 system have provided abundant resources for functional genomics and crop breeding. However, because of the complexity, it is a big challenge to accomplish large-scale targeted mutagenesis...
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Method: Probabilistic association of differentially expressed genes with cis-regulatory elements
- Brian S. Roberts,
- Ashlyn G. Anderson,
- E. Christopher Partridge,
- Gregory M. Cooper,
- and Richard M. Myers
Genome Res. April 2024 34: 620-632; Published in Advance April 17, 2024, doi:10.1101/gr.278598.123
..., establishing good performance by DegCre that is comparable or superior to competing methods. DegCre is a novel approach to the association of CREs to genes from a perturbation-differential perspective, with strengths that are complementary to existing approaches and allow for new insights into gene regulation...
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Method: Identifying genes within pathways in unannotated genomes with PaGeSearch
- Sohyoung Won,
- Jaewoong Yu,
- and Heebal Kim
Genome Res. May 2024 34: 784-795; Published in Advance June 10, 2024, doi:10.1101/gr.278566.123
...in the (Li 2023).Biological pathways are networks of interconnected genes and molecules that coordinate and regulate various biological processes within cells, tissues, and organisms. By identifying the genes present in a pathway, researchers can gain insights into their collective functions and how...
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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
...Construction and evaluation of a new rat reference assembly, GRCr8, from long reads and long-range scaffolding Kai Li1, Melissa L. Smith2, J. Chris Blazier3, Kelli J. Kochan3, Jonathan M.D. Wood4, Kerstin Howe4, Anne E. Kwitek5, Melinda R. Dwinell5, Hao Chen6, Julia L. Ciosek1, Patrick Masterson7...
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Method: Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT
- Andrea Cracco and
- Alexandru I. Tomescu
Genome Res. July 2023 33: 1198-1207; Published in Advance May 30, 2023, doi:10.1101/gr.277615.122
...Bruijn graphs are one of the most fundamental data structures in computational genomics. Colored compacted de Bruijn graphs are a variant built on a collection of sequences and associate to each k-mer the sequences in which it appears. We present GGCAT, a tool for constructing both types of graphs, based...
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Method: Power-law behavior of transcriptional bursting regulated by enhancer–promoter communication
- Zihao Wang,
- Zhenquan Zhang,
- Songhao Luo,
- Tianshou Zhou,
- and Jiajun Zhang
Genome Res. January 2024 34: 106-118; Published in Advance January 3, 2024, doi:10.1101/gr.278631.123
...Power-law behavior of transcriptional bursting regulated by enhancer–promoter communication Zihao Wang1,2,3, Zhenquan Zhang1,2,3, Songhao Luo1,2,3, Tianshou Zhou1,2 and Jiajun Zhang1,2 1Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China...
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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
...successful dorsal/ventral patterning and neuronal differentiation. We identified 363 differentially expressed genes (DEGs) in KO dNPCs compared to isogenic parental dNPCs (Fig. 3D) and 287 DEGs in vNPCs (Supplemental Fig. S6B,C; Supplemental Table S2). The 277 up-regulated genes in KO dNPCs showed enrichment...

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