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Method: A best-match approach for gene set analyses in embedding spaces
- Lechuan Li,
- Ruth Dannenfelser,
- Charlie Cruz,
- and Vicky Yao
Genome Res. September 2024 34: 1421-1433; Published in Advance September 4, 2024, doi:10.1101/gr.279141.124
...embeddings for downstream machine-learning tasks. Much less has been done to examine the embeddings directly, especially analyses of gene sets in embedding spaces. Here, we propose an Algorithm for Network Data Embedding and Similarity (ANDES), a novel best-match approach that can be used with existing gene...
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LETTER: Genomic clusters, putative pathogen recognition molecules, and antimicrobial genes are induced by infection of C. elegans with M. nematophilum
- Delia O’Rourke,
- Dilair Baban,
- Maria Demidova,
- Richard Mott,
- and Jonathan Hodgkin
Genome Res. August 2006 16: 1005-1016; Published in Advance June 29, 2006, doi:10.1101/gr.50823006
...clusters within the . Using the algorithm described in the Methods section, we identified 18 spatial clusters of genes in which the sum of the genes’ log ratios was significantly larger than would be expected by chance on a -wide basis (Supplemental Data S2; up-regulated and down-regulated clusters...
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Letter: Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved
- Itai Yanai and
- Craig P. Hunter
Genome Res. December 2009 19: 2214-2220; Published in Advance September 10, 2009, doi:10.1101/gr.093815.109
...of coexpressed gene neighbors in C. briggsae and asked whether the C. elegans orthologs are also coexpressed. We found that the general level of expression similarity was dramatically lower, despite examining only C. elegans orthologs within conserved gene neighborhoods (Fig. 4A). We next examined those C...
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Methods: Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics
- Yueyi Liu,
- X. Shirley Liu,
- Liping Wei,
- Russ B. Altman,
- and Serafim Batzoglou
Genome Res. March 2004 14: 451-458; doi:10.1101/gr.1327604
..., Srf, and Sp1 from a set of human-muscle-specific genes. It also discovered the NFAT motif from genes up-regulated by CD28 stimulation in T-cells, which implies the direct involvement of NFAT in mediating the CD28 stimulatory signal. Using Caenorhabditis elegans – Caenorhabditis briggsae comparison...
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Research: Dynamic DNA N⁶-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus
- Yongqiang Liu,
- Junhua Niu,
- Fei Ye,
- Therese Solberg,
- Borong Lu,
- Chundi Wang,
- Mariusz Nowacki,
- and Shan Gao
Genome Res. February 2024 34: 256-271; Published in Advance March 12, 2024, doi:10.1101/gr.278796.123
...to external stress in an expanding list of eukaryotes: It is involved in mitochondrial stress adaptation in the worm Caenorhabditis elegans (Ma et al. 2019), the expression of neuronal genes in the fly Drosophila melanogaster (Yao et al. 2018), salt and temperature tolerance in the rice Oryza sativa (Zhang et...
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Research: Distinct types of short open reading frames are translated in plant cells
- Igor Fesenko,
- Ilya Kirov,
- Andrey Kniazev,
- Regina Khazigaleeva,
- Vassili Lazarev,
- Daria Kharlampieva,
- Ekaterina Grafskaia,
- Viktor Zgoda,
- Ivan Butenko,
- Georgy Arapidi,
- Anna Mamaeva,
- Vadim Ivanov,
- and Vadim Govorun
Genome Res. September 2019 29: 1464-1477; Published in Advance August 6, 2019, doi:10.1101/gr.253302.119
...of thousands of short open reading frames (sORFs; <100 codons) whose coding potential has been the subject of recent reviews (Andrews and Rothnagel 2014; Couso 2015; Hellens et al. 2016; Couso and Patraquim 2017; Rothnagel and Menschaert 2018; Ruiz-Orera and Albà 2019). However, gene annotation algorithms...
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Research: The identification and functional annotation of RNA structures conserved in vertebrates
- Stefan E. Seemann,
- Aashiq H. Mirza,
- Claus Hansen,
- Claus H. Bang-Berthelsen,
- Christian Garde,
- Mikkel Christensen-Dalsgaard,
- Elfar Torarinsson,
- Zizhen Yao,
- Christopher T. Workman,
- Flemming Pociot,
- Henrik Nielsen,
- Niels Tommerup,
- Walter L. Ruzzo,
- and Jan Gorodkin
Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
...ones. For selected human and mouse candidate pairs, qRT-PCR and in vitro RNA structure probing supported both shared expression and shared structure despite low abundance and low sequence identity. About 30,000 CRS regions are located near coding or long noncoding RNA genes or within enhancers...
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RESOURCE: A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands
- Cosmas Giallourakis,
- Zhifang Cao,
- Todd Green,
- Heather Wachtel,
- Xiaohui Xie,
- Marco Lopez-Illasaca,
- Mark Daly,
- John Rioux,
- and Ramnik Xavier
Genome Res. August 2006 16: 1056-1072 ; Published in Advance July 6, 2006, doi:10.1101/gr.5285206
...a transmembrane (TM) domain by the TMHMM algorithm is shown ( Krogh et al. 2001 ). Step (5): Pairwise relationships among PDZ domain-encoding genes and the PDZCBM gene set are determined from correlated mRNA levels, cellular localization, and common literature co-citation patterns between a PDZ gene and potential...
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ENSEMBL Special: Sockeye: A 3D Environment for Comparative Genomics
- Stephen B. Montgomery,
- Tamara Astakhova,
- Mikhail Bilenky,
- Ewan Birney,
- Tony Fu,
- Maik Hassel,
- Craig Melsopp,
- Marcin Rak,
- A. Gordon Robertson,
- Monica Sleumer,
- Asim S. Siddiqui,
- and Steven J.M. Jones
Genome Res. May 2004 14: 956-962; doi:10.1101/gr.1890304
...( HD ) from LAGAN ( top four sequence tracks) and ClustalW ( bottom four sequence tracks). The sequence tracks in order are (1) mouse, (2) rat, (3) human, (4) Fugu, (5) mouse, (6) rat, (7) human, and (8) Fugu. For the LAGAN algorithm, the start of translation of the HD gene in each species aligns...
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PERSPECTIVE: Changing perspectives in yeast research nearly a decade after the genome sequence
- Kara Dolinski and
- David Botstein
Genome Res. December 2005 15: 1611-1619; doi:10.1101/gr.3727505
...clustering algorithms and data visualization tools to allow for analysis and presentation of the large volume of microarray results. An early approach, which is still probably one of the most popular, is the application of hierarchical clustering to group similarly expressed genes together, representing...

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