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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...(via CATH, see Methods; note “paralog” refers to genes present in the human not to copies arising from duplication events such as WGD). Filtering steps removed FIEs identified in genes without significant expression in TRACERx lung tumors (LUAD, 3/80 genes; LUSC, 4/41 genes) or where the FunVar score...
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Research: The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores
- Yulong Liu,
- Gang Zhai,
- Jingzhi Su,
- Yulong Gong,
- Bingyuan Yang,
- Qisheng Lu,
- Longwei Xi,
- Yutong Zheng,
- Jingyue Cao,
- Haokun Liu,
- Junyan Jin,
- Zhimin Zhang,
- Yunxia Yang,
- Xiaoming Zhu,
- Zhongwei Wang,
- Gaorui Gong,
- Jie Mei,
- Zhan Yin,
- Rodolphe E. Gozlan,
- Shouqi Xie,
- and Dong Han
Genome Res. July 2024 34: 981-996; Published in Advance August 9, 2024, doi:10.1101/gr.278476.123
...(yellow to red represents low to high intensity). (C) Visualization of the whole- alignment is shown using the Circos plot (Krzywinski et al. 2009). Outer to the inner circles: chromosome length (each tick mark represents 1/5 Mb), gene density, GC percentage distribution (in nonoverlapping 100 kb windows...
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Method: Predicting genetic modifier loci using functional gene networks
- Insuk Lee,
- Ben Lehner,
- Tanya Vavouri,
- Junha Shin,
- Andrew G. Fraser,
- and Edward M. Marcotte
Genome Res. August 2010 20: 1143-1153; Published in Advance June 9, 2010, doi:10.1101/gr.102749.109
...gene pairs were identified based on the data associated with the orthologs of the C. elegans genes (‘‘associalogs’’) (Lee et al. 2008). A total of 14 linkage sets were analyzed based on datasets previously incorporated into gene networks for yeast (seven sets from YeastNet; Lee et al. 2007), human (six...
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Research: Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis
- Weisheng Wu,
- Christapher S. Morrissey,
- Cheryl A. Keller,
- Tejaswini Mishra,
- Maxim Pimkin,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2014 24: 1945-1962; Published in Advance October 15, 2014, doi:10.1101/gr.164830.113
...in mouse hematopoiesis Genome Research 1949 www..org and Cbfa2t3, encoding a core-binding factor whose ortholog in humans is rearranged in some leukemias. Examples of presumptive target genes associated with proliferation include those encoding growth factors and receptors such as VEGFA and its receptor...
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RESOURCE: The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC) Genome Res. October 15, 2004 14: 2121-2127; doi:10.1101/gr.2596504

...in the reference , and links from this track can show the alignment of the cDNA with the reference sequence. All of the search and visualization functionality of this browser can be used to identify genes with MGC clones and to provide additional information about the corresponding genes, including the gene...
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Research: The genomic basis of evolutionary differentiation among honey bees
- Bertrand Fouks,
- Philipp Brand,
- Hung N. Nguyen,
- Jacob Herman,
- Francisco Camara,
- Daniel Ence,
- Darren E. Hagen,
- Katharina J. Hoff,
- Stefanie Nachweide,
- Lars Romoth,
- Kimberly K.O. Walden,
- Roderic Guigo,
- Mario Stanke,
- Giuseppe Narzisi,
- Mark Yandell,
- Hugh M. Robertson,
- Nikolaus Koeniger,
- Panuwan Chantawannakul,
- Michael C. Schatz,
- Kim C. Worley,
- Gene E. Robinson,
- Christine G. Elsik,
- and Olav Rueppell
Genome Res. July 2021 31: 1203-1215; Published in Advance May 4, 2021, doi:10.1101/gr.272310.120
...with homology with the X, Y, and Z GR pseudogenes. Six of 11 GRs with a length of at least 300 amino acids contained premature stop codons, whereas the other five represent new, potentially functional GRs.To validate potential functionality of the newly described GRs, we visualized gene models along with RNA...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...and C. briggsaeTo understand intra- and interspecific divergences at the gene family level, we classified orthologous gene families in the two species using OrthoFinder (Emms and Kelly 2019). We identified a total of 24,690 orthologous gene families in the C. nigoni strains, of which 69% (17,095) were...
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Resource: Epigenomics of embryogenesis in turbot
- Oscar Aramburu,
- Belen G Pardo,
- Ada Jimenez-Gonzalez,
- Andrés Blanco-Hortas,
- Daniel Macqueen,
- Carmen Bouza,
- and Paulino Martinez
Genome Res. November 4, 2025 gr.280355.124; Published in Advance November 4, 2025, doi:10.1101/gr.280355.124
...; Theocharidis et al., 2009) 142 were applied to visualize the expression changes across development. The 143 correlation network shows a “pulley-arch” structure, where the clusters ordered 144 from left to right of the graph represent genes expressed at early, mid and late 145 development stages, respectively...
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Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
- Zepu Miao and
- Jia-Xing Yue
Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
...data set, users can interactively visualize, navigate, and query the pan graph via a primary linear reference–based coordinate system. An example of the human APOE gene region (Chr 19: 44,905,000–44,910,000, GRCh38 coordinates) of the HRPC Minigraph-Cactus pan graph is shown here. The APOE gene bears...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...) Anterior foregut; (PFG) posterior foregut; (MHG) mid/hindgut; (PP) pancreatic progenitors. Zebrafish have multiple orthologs of mammalian TF genes owing to the additional whole and other small duplications during teleost evolution. Where present, a, b, and c paralogs are depicted. (*) Although the enriched...

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