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Article
Hyperlipidemia-induced hematopoiesis is repressed by MLKL in endothelial cells of the splenic niche
Dysregulation of the hematopoietic niche during hyperlipidemia facilitates pathologic leukocyte production, driving atherogenesis. Although definitive hematopoiesis occurs primarily in the bone marrow, during ...
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Article
Open AccessSparse data embedding and prediction by tropical matrix factorization
Matrix factorization methods are linear models, with limited capability to model complex relations. In our work, we use tropical semiring to introduce non-linearity into matrix factorization models. We propose...
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Article
Open AccessRanking cancer drivers via betweenness-based outlier detection and random walks
Recent cancer genomic studies have generated detailed molecular data on a large number of cancer patients. A key remaining problem in cancer genomics is the identification of driver genes.
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Article
Open AccessDriveWays: a method for identifying possibly overlap** driver pathways in cancer
The majority of the previous methods for identifying cancer driver modules output nonoverlap** modules. This assumption is biologically inaccurate as genes can participate in multiple molecular pathways. Thi...
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Article
Life cycle assessment of cotton woven shirts and alternative manufacturing techniques
In this study, the life cycle assessment of cotton woven shirt production, from cotton cultivation to the final product, has been done. In this scope, four alternative production scenarios were developed and e...
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Article
Open AccessPredicting clinical outcomes in neuroblastoma with genomic data integration
Neuroblastoma is a heterogeneous disease with diverse clinical outcomes. Current risk group models require improvement as patients within the same risk group can still show variable prognosis. Recently collect...
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Article
Open AccessA comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer)
RNA molecules fold into complex three-dimensional shapes, guided by the pattern of hydrogen bonding between nucleotides. This pattern of base pairing, known as RNA secondary structure, is critical to their cel...
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Article
Open AccessQuaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression
A hallmark of inflammatory diseases is the excessive recruitment and influx of monocytes to sites of tissue damage and their ensuing differentiation into macrophages. Numerous stimuli are known to induce trans...
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Article
A compendium of RNA-binding motifs for decoding gene regulation
RNA-binding proteins are key regulators of gene expression, yet only a small fraction have been functionally characterized. Here we report a systematic analysis of the RNA motifs recognized by RNA-binding prot...
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Article
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
Until now, determining the sequences recognized by an RNA-binding protein has been time and labor intensive. Ray et al. use a custom pool of >210,000 oligos that encode linear and stem-loop RNAs to rapidly determ...
