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Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...to be complementarity in the recovery of real protein-coding sequences between the methods (based upon BUSCO recovery), consider using an approach to integrate predictions. In conclusion, the longer-term challenge for building annotations across the tree of life is to make methodological advances suggested above...
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Research: Meta-analysis of human and mouse ALS astrocytes reveals multi-omic signatures of inflammatory reactive states
- Oliver J. Ziff,
- Benjamin E. Clarke,
- Doaa M. Taha,
- Hamish Crerar,
- Nicholas M. Luscombe,
- and Rickie Patani
Genome Res. January 2022 32: 71-84; Published in Advance December 28, 2021, doi:10.1101/gr.275939.121
...://shiny.crick.ac.uk/ALS_reactive_astrocytes_meta/).View larger version: In this window In a new window Figure 5. Working model. Multi-omic signatures of healthy astrocytes (left, blue) and ALS astrocytes (right, red).We identified overlapping signatures between inflammatory reactive astrocytes and ALS mutant astrocytes, characterized by common up...
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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: EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow
- Wagner C.S. Magalhães,
- Nathalia M. Araujo,
- Thiago P. Leal,
- Gilderlanio S. Araujo,
- Paula J.S. Viriato,
- Fernanda S. Kehdy,
- Gustavo N. Costa,
- Mauricio L. Barreto,
- Bernardo L. Horta,
- Maria Fernanda Lima-Costa,
- Alexandre C. Pereira,
- Eduardo Tarazona-Santos,
- Maíra R. Rodrigues,
- and The Brazilian EPIGEN Consortium
Genome Res. July 2018 28: 1090-1095; Published in Advance June 14, 2018, doi:10.1101/gr.225458.117
...Natl Acad Sci 112: 8696–8701. ↵Kolker E, Ozdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, et al. 2014. Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. OMICS 18: 10–14. ↵Lima-Costa MF...
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Resource: Benchmark and integration of resources for the estimation of human transcription factor activities
- Luz Garcia-Alonso,
- Christian H. Holland,
- Mahmoud M. Ibrahim,
- Denes Turei,
- and Julio Saez-Rodriguez
Genome Res. August 2019 29: 1363-1375; Published in Advance July 24, 2019, doi:10.1101/gr.240663.118
...-curated information followed by ChIP-seq data. We provide an integrated resource of all TF–target interactions derived through these strategies, with confidence scores, as a resource for enhanced prediction of TF activities.The regulation of gene expression programs is fundamental for cell development...
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Method: Principled multi-omic analysis reveals gene regulatory mechanisms of phenotype variation
- Casey Hanson,
- Junmei Cairns,
- Liewei Wang,
- and Saurabh Sinha
Genome Res. August 2018 28: 1207-1216; Published in Advance June 13, 2018, doi:10.1101/gr.227066.117
...differences. In this study, we develop a new probabilistic model, called pGENMi, that integrates multi-omic data to investigate the transcriptional regulatory mechanisms underlying interindividual variation of a specific phenotype—that of cell line response to cytotoxic treatment. In particular, p...
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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
...originate from different oncogenic events.In summary, the multi-omics data in the present study offer a valuable resource to study the mechanisms of liver organogenesis, development, and tools to understand liver tumorigenesis, from the origins of cancer cells to metastasis.MethodsAnimals and tissue...
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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
...environment. We showed the differentially expressed genes between the two haploids in hybrid were associated with either genetic or epigenetic effects. In summary, our multi-omics data from the hybrid mice provided haploid-specific information on the 3D nuclear architecture and a rich resource for further...
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Resource: Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland
- Sandra Reuter,
- M. Estée Török,
- Matthew T.G. Holden,
- Rosy Reynolds,
- Kathy E. Raven,
- Beth Blane,
- Tjibbe Donker,
- Stephen D. Bentley,
- David M. Aanensen,
- Hajo Grundmann,
- Edward J. Feil,
- Brian G. Spratt,
- Julian Parkhill,
- and Sharon J. Peacock
Genome Res. February 2016 26: 263-270; Published in Advance December 15, 2015, doi:10.1101/gr.196709.115
...in antibiotic resistance profiles, with examples of local expansion, as well as widespread circulation of mobile genetic elements across the bacterial population.Wehave generated a resource for the future surveillance andoutbreak investigation ofMRSA in theUnitedKingdom and Ireland and have shown the value...
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Corrigendum: Corrigendum: Benchmark and integration of resources for the estimation of human transcription factor activities
- Luz Garcia-Alonso,
- Christian H. Holland,
- Mahmoud M. Ibrahim,
- Denes Turei,
- and Julio Saez-Rodriguez
Genome Res. April 2021 31: 745; doi:10.1101/gr.275408.121
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