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Method: Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet
- Chuanyuan Wang and
- Zhi-Ping Liu
Genome Res. February 2025 35: 340-354; Published in Advance December 18, 2024, doi:10.1101/gr.279551.124
...SEM, GRISLI, GENIE3, SCODE, and SINCERITIES (which DigNet surpasses by 6.5% to 11%) is under random predictions, suggesting their inability to accurately infer gene networks from breast cancer scRNA-seq data. The ARACNE, CLR, PIDC, GRNboost2, and Tigress algorithms can infer some proper regulatory...
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Research: Limited allele-specific gene expression in highly polyploid sugarcane
- Gabriel Rodrigues Alves Margarido,
- Fernando Henrique Correr,
- Agnelo Furtado,
- Frederik C. Botha,
- and Robert James Henry
Genome Res. February 2022 32: 297-308; Published in Advance December 23, 2021, doi:10.1101/gr.275904.121
...for a substantial number of indels to be present. After filtering out low-quality polymorphisms 5,748,251 biallelic SNVs remained. Classifying these sites based on their predicted impact on gene structures resulted in the following distribution of predicted effects: 13,619,337 (79.82%) modifier effects, 1...
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Resource: mGene: Accurate SVM-based gene finding with an application to nematode genomes
- Gabriele Schweikert,
- Alexander Zien,
- Georg Zeller,
- Jonas Behr,
- Christoph Dieterich,
- Cheng Soon Ong,
- Petra Philips,
- Fabio De Bona,
- Lisa Hartmann,
- Anja Bohlen,
- Nina Krüger,
- Sören Sonnenburg,
- and Gunnar Rätsch
Genome Res. November 2009 19: 2133-2143; Published in Advance June 29, 2009, doi:10.1101/gr.090597.108
...features within very small windows (6–30 bp) with SVMs and simple quadratic kernels considering second order relations. Well-designed features describing multiple alignments, a strength of Conrad and Contrast inmany applications, appear to be less crucial for nematode gene predictions. (3) The integrative...
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Research: Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania
- Matthew B. Rogers,
- James D. Hilley,
- Nicholas J. Dickens,
- Jon Wilkes,
- Paul A. Bates,
- Daniel P. Depledge,
- David Harris,
- Yerim Her,
- Pawel Herzyk,
- Hideo Imamura,
- Thomas D. Otto,
- Mandy Sanders,
- Kathy Seeger,
- Jean-Claude Dujardin,
- Matthew Berriman,
- Deborah F. Smith,
- Christiane Hertz-Fowler,
- and Jeremy C. Mottram
Genome Res. December 2011 21: 2129-2142; Published in Advance October 28, 2011, doi:10.1101/gr.122945.111
...amplification may contribute to alterations in gene expression in response to environmental conditions in the host, providing a genetic basis for disease tropism. Footnotes ↵ 10 Corresponding authors. E-mail C.Hertz-Fowler@liverpool.ac.uk . E-mail jeremy...
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Research: A recombination hotspot leads to sequence variability within a novel gene (AK005651) and contributes to type 1 diabetes susceptibility
- Iris K.L. Tan,
- Leanne Mackin,
- Nancy Wang,
- Anthony T. Papenfuss,
- Colleen M. Elso,
- Michelle P. Ashton,
- Fiona Quirk,
- Belinda Phipson,
- Melanie Bahlo,
- Terence P. Speed,
- Gordon K. Smyth,
- Grant Morahan,
- and Thomas C. Brodnicki
Genome Res. December 2010 20: 1629-1638; Published in Advance November 4, 2010, doi:10.1101/gr.101881.109
...hotspot that generated four crossover breakpoints, including one with a complex conversion tract. The Idd11 haplotype and recombination hotspot are located within a predicted gene of unknown function, which exhibits decreased expression in relevant tissues of NOD mice. Notably, it was the recombination...
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Research: High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: Alternative expression modes and gene function correlates
- Jun Matsumoto,
- Ken Dewar,
- Jessica Wasserscheid,
- Graham B. Wiley,
- Simone L. Macmil,
- Bruce A. Roe,
- Robert W. Zeller,
- Yutaka Satou,
- and Kenneth E.M. Hastings
Genome Res. May 2010 20: 636-645; Published in Advance March 8, 2010, doi:10.1101/gr.100271.109
...Caenorhabditis, outrons (and introns) are A+T-rich compared with exons (Csank et al. 1990; Conrad et al. 1991). Upstream segments of 50 nt or 20 nt were also more pyrimidine-rich (;57% C+T) than corresponding Table 1. Ciona KH gene loci represented by >1000 SL-PCR reads Rank Locus name Protein name Total reads 1...
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Method: Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
- Michael Stevens,
- Jeffrey B. Cheng,
- Daofeng Li,
- Mingchao Xie,
- Chibo Hong,
- Cécile L. Maire,
- Keith L. Ligon,
- Martin Hirst,
- Marco A. Marra,
- Joseph F. Costello,
- and Ting Wang
Genome Res. September 2013 23: 1541-1553; Published in Advance June 26, 2013, doi:10.1101/gr.152231.112
...levels of these ICRs based on MethylC-seq and methylCRF. (B) Same as A, except for fetal NSCs. (C ) A Genome Browser view of ICR near gene MEST (mesoderm specific transcript, chr7). (D) A Genome Browser view of ICR near gene NDN (necdin, chr15). methylCRF predicts single-CpG-resolution methylome Genome...
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Methods: Genome-wide discovery of human heart enhancers
- Leelavati Narlikar,
- Noboru J. Sakabe,
- Alexander A. Blanski,
- Fabio E. Arimura,
- John M. Westlund,
- Marcelo A. Nobrega,
- and Ivan Ovcharenko
Genome Res. March 2010 20: 381-392; Published in Advance January 14, 2010, doi:10.1101/gr.098657.109
...(top three genomic regions), while genes repressed or not expressed in the heart have fewer predictions in their loci. (All elements in the training set are excluded in these figures.) Computational prediction of cardiac enhancers Genome Research 387 www..org random genomic integration event. Embryos...
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Resource: Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster
- Federico A. Santoni,
- Periklis Makrythanasis,
- Sergey Nikolaev,
- Michel Guipponi,
- Daniel Robyr,
- Armand Bottani,
- and Stylianos E. Antonarakis
Genome Res. February 2014 24: 349-355; Published in Advance January 3, 2014, doi:10.1101/gr.163832.113
...validated de novo variants, of which one is germline and five are somatic variants generated ‘‘by the age of the cell lines (number of passages), the mutagenicity of the cell culture conditions, and/or the clonality of the cell lines’’ (Conrad et al. 2011). RawBAM fileswere processed as reported...
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Methods: Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time
- Nathalie Harder,
- Felipe Mora-Bermúdez,
- William J. Godinez,
- Annelie Wünsche,
- Roland Eils,
- Jan Ellenberg,
- and Karl Rohr
Genome Res. November 2009 19: 2113-2124; Published in Advance October 1, 2009, doi:10.1101/gr.092494.109
...), Gene Expression and Cell Biology/Biophysics Programmes, D-69117 Heidelberg, Germany ↵ 4 Present address: Max Planck Institute of Molecular Cell Biology and Genetics, (MPI-CBG), Pfotenhauerstrasse 108, D-01307 Dresden, Germany. ↵ 3 These authors contributed equally...

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