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Method: Balancing gene ontology annotation specificity in protein function prediction based on the protein sequence large graph
- Jiangyi Shao,
- Shutao Chen,
- Ziwen Wang,
- Zixu Chen,
- and Bin Liu
Genome Res. April 15, 2026 gr.280816.125; Published in Advance April 15, 2026, doi:10.1101/gr.280816.125
...Balancing Gene Ontology annotation specificity in protein function prediction 1 based on the protein sequence large graph 2 Jiangyi Shao1,2, Shutao Chen1, Ziwen Wang 1, Zixu Chen1,2, Bin Liu1,2* 3 1 School of Computer Science and Technology, Beijing Institute of Technology, 4 Beijing 100081, China...
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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
...appropriate therapy choice and timing (Black and McGranahan 2021; Fisk et al. 2022).Gene duplication during species evolution is an important mechanism that permits genetic diversity and the development of new functions through drift and selection (Ohno 1970; Taylor and Raes 2004). Duplicated genes...
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Research: ceRNA crosstalk mediated by ncRNAs is a novel regulatory mechanism in fish sex determination and differentiation
- Lili Tang,
- Fei Huang,
- Wuxin You,
- Ansgar Poetsch,
- Rafael Henrique Nóbrega,
- Deborah Mary Power,
- Tengfei Zhu,
- Kaiqiang Liu,
- Hong-Yan Wang,
- Qian Wang,
- Xiwen Xu,
- Bo Feng,
- Manfred Schartl,
- and Changwei Shao
Genome Res. August 2022 32: 1502-1515; Published in Advance August 12, 2022, doi:10.1101/gr.275962.121
....uni-wuerzburg.de, shaocw@ysfri.ac.cnAbstractCompeting endogenous RNAs (ceRNAs) are vital regulators of gene networks in mammals. The involvement of noncoding RNAs (ncRNAs) as ceRNA in genotypic sex determination (GSD) and environmental sex determination (ESD) in fish is unknown. The Chinese tongue sole, which has both GSD...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...33 and 11 species, respectively (Figs. 2, 3A,E). Not all species for which RNA-seq data were available were selected for these data sets, as the selection needed to balance the many requirements for gene expression analysis (reproducible kidney dissection, RNA quality and batch effect, number...
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Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
- Robin Kosch,
- Katharina Limm,
- Annette M. Staiger,
- Nadine S. Kurz,
- Nicole Seifert,
- Bence Oláh,
- Stefan Solbrig,
- Viola Poeschel,
- Gerhard Held,
- Marita Ziepert,
- Norbert Schmitz,
- Emil Chteinberg,
- Reiner Siebert,
- Rainer Spang,
- Helena U. Zacharias,
- German Ott,
- Peter J. Oefner,
- and Michael Altenbuchinger
Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
...-translational modifications (CTMs/PTMs). Yet, it remains an open question how to holistically explore such data and their relationship to complementary omics/phenotypic information. Graphical models are particularly suited to study molecular networks and underlying regulatory mechanisms, as they can distinguish direct from...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species Daniel Siqueira de Oliveira1,2,3, Anaïs Larue2, William Vilas Boas Nunes2, Francois Sabot4, Alejandra Bodelón5, María Pilar García Guerreiro5, Cristina Vieira2 and Claudia Marcia...
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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
...for each species partitioned according to their orthology profiles. A. florea possessed the greatest number of lineage-specific genes followed by A. mellifera.Genome-wide patterns of positive selectionTo identify positive selection that acted on protein-coding genes during the evolution of honey bees, we...
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Method: Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts
- Irmgard U. Haussmann,
- Thomas C. Dix,
- David W.J. McQuarrie,
- Veronica Dezi,
- Abdullah I. Hans,
- Roland Arnold,
- and Matthias Soller
Genome Res. December 2024 34: 2279-2292; Published in Advance December 3, 2024, doi:10.1101/gr.279479.124
...selection of efficient sgRNAs, we developed web-based PlatinumCRISPr, an sgRNA design tool to evaluate base-pairing and sequence composition parameters for optimal design of highly efficient sgRNAs for Cas9 editing. We applied this tool to select sgRNAs to efficiently generate gene deletions in Drosophila...
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Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
....0022) in their s, which is an indication of balancing selection (Charlesworth 2006). The genetic diversity of the same window in Orkney voles is close to zero (π = 4.5 × 10−5). Therefore, we cannot completely exclude the possibility that reduced efficacy of balancing selection on MHC II genes, either owing...
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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
...activator of ARL3 GTPase (RP2) gene (Machado et al. 2014), utilizing their polymorphic repeats for parental allele identification (Caylor 2023). The ratio of inactivation between the two alleles can determine whether XCI is random (balanced) or skewed (nonrandom) (Amos-Landgraf et al. 2006). Skewed XCI can...
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