Stikker, Bernard S Stik, Grégoire van Ouwerkerk, Antoinette F Trap, Lianne Spicuglia, Salvatore Hendriks, Rudi W Stadhouders, Ralph
Published in
Genome biology
Genome-wide association studies have identified 3p21.31 as the main risk locus for severe COVID-19, although underlying mechanisms remain elusive. We perform an epigenomic dissection of 3p21.31, identifying a CTCF-dependent tissue-specific 3D regulatory chromatin hub that controls the activity of several chemokine receptor genes. Risk SNPs colocali...
Zhang, Ping Amarasinghe, Harindra E. Whalley, Justin P. Tay, Chwen Fang, Hai Migliorini, Gabriele Brown, Andrew C. Allcock, Alice Scozzafava, Giuseppe Rath, Phalguni
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Published in
Genome Biology
Background Chromatin states and enhancers associate gene expression, cell identity and disease. Here, we systematically delineate the acute innate immune response to endotoxin in terms of human macrophage enhancer activity and contrast with endotoxin tolerance, profiling the coding and non-coding transcriptome, chromatin accessibility and epigeneti...
Xu, Zhongli Heidrich-O'Hare, Elisa Chen, Wei Duerr, Richard H
Published in
Genome biology
The recently developed method TEA-seq and similar DOGMA-seq single cell trimodal omics assays provide unprecedented opportunities for understanding cell biology, but independent evaluation is lacking. We explore the utility of DOGMA-seq compared to the bimodal CITE-seq assay in activated and stimulated human peripheral blood T cells. We find that s...
Fancello, Laura Burger, Thomas
Published in
Genome Biology
Background Proteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- or genome-derived custom protein databases. However, empirical observations reveal that these large proteogenomic databases produce lower-sensitivity peptide identifications. Various strategies have been proposed to avoid this...
Balaji, Advait Kille, Bryce Kappell, Anthony D. Godbold, Gene D. Diep, Madeline Elworth, R. A. Leo Qian, Zhiqin Albin, Dreycey Nasko, Daniel J. Shah, Nidhi
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Published in
Genome Biology
The COVID-19 pandemic has emphasized the importance of accurate detection of known and emerging pathogens. However, robust characterization of pathogenic sequences remains an open challenge. To address this need we developed SeqScreen, which accurately characterizes short nucleotide sequences using taxonomic and functional labels and a customized s...
Brandes, Nadav Weissbrod, Omer Linial, Michal
Published in
Genome Biology
Genetic studies of human traits have revolutionized our understanding of the variation between individuals, and yet, the genetics of most traits is still poorly understood. In this review, we highlight the major open problems that need to be solved, and by discussing these challenges provide a primer to the field. We cover general issues such as po...
Tang, Daiwei Park, Seyoung Zhao, Hongyu
Published in
Genome biology
A challenge in bulk gene differential expression analysis is to differentiate changes due to cell type-specific gene expression and cell type proportions. SCADIE is an iterative algorithm that simultaneously estimates cell type-specific gene expression profiles and cell type proportions, and performs cell type-specific differential expression analy...
Zhou, Yanli Zhang, Chengjun Zhang, Li Ye, Qiannan Liu, Ningyawen Wang, Muhua Long, Guangqiang Fan, Wei Long, Manyuan Wing, Rod A
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Published in
Genome biology
Events of gene fusion have been reported in several organisms. However, the general role of gene fusion as part of new gene origination remains unknown. We conduct genome-wide interrogations of four Oryza genomes by designing and implementing novel pipelines to detect fusion genes. Based on the phylogeny of ten plant species, we detect 310 fusion g...
Karimzadeh, Mehran Hoffman, Michael M
Published in
Genome biology
Existing methods for computational prediction of transcription factor (TF) binding sites evaluate genomic regions with similarity to known TF sequence preferences. Most TF binding sites, however, do not resemble known TF sequence motifs, and many TFs are not sequence-specific. We developed Virtual ChIP-seq, which predicts binding of individual TFs ...
Markowska, Magda Cąkała, Tomasz Miasojedow, BłaŻej Aybey, Bogac Juraeva, Dilafruz Mazur, Johanna Ross, Edith Staub, Eike Szczurek, Ewa
Published in
Genome biology
Copy number alterations constitute important phenomena in tumor evolution. Whole genome single-cell sequencing gives insight into copy number profiles of individual cells, but is highly noisy. Here, we propose CONET, a probabilistic model for joint inference of the evolutionary tree on copy number events and copy number calling. CONET employs an ef...
