Search results for: Joshua D. Welch

Items from 1 to 5 out of 5 results

article

Intercellular Interactions of an Adipogenic CXCL12‐Expressing Stromal Cell Subset in Murine Bone Marrow

Yuki Matsushita, Angel Ka Yan Chu, Wanida Ono, Joshua D Welch, more

Journal of Bone and Mineral Research > 36 > 6 > 1145 - 1158

Bone marrow houses a multifunctional stromal cell population expressing C‐X‐C motif chemokine ligand 12 (CXCL12), termed CXCL12‐abundant reticular (CAR) cells, that regulates osteogenesis and adipogenesis. The quiescent pre‐adipocyte‐like subset of CXCL12⁺ stromal cells (“Adipo‐CAR” cells) is localized to sinusoidal surfaces and particularly enriched for hematopoiesis‐supporting cytokines. However,...

article

MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

Joshua D. Welch, Alexander J. Hartemink, Jan F. Prins

Genome Biology > 2017 > 18 > 1 > 1-19

Single cell experimental techniques reveal transcriptomic and epigenetic heterogeneity among cells, but how these are related is unclear. We present MATCHER, an approach for integrating multiple types of single cell measurements. MATCHER uses manifold alignment to infer single cell multi-omic profiles from transcriptomic and epigenetic measurements performed on different cells of the same type. Using...

article

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data

Joshua D. Welch, Alexander J. Hartemink, Jan F. Prins

Genome Biology > 2016 > 17 > 1 > 1-15

Single cell experiments provide an unprecedented opportunity to reconstruct a sequence of changes in a biological process from individual “snapshots” of cells. However, nonlinear gene expression changes, genes unrelated to the process, and the possibility of branching trajectories make this a challenging problem. We develop SLICER (Selective Locally Linear Inference of Cellular Expression Relationships)...

article

Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

Joshua D Welch, Jeanette Baran-Gale, Charles M Perou, Praveen Sethupathy, more

BMC Genomics > 2015 > 16 > 1 > 1-16

Background Recent studies have shown that some pseudogenes are transcribed and contribute to cancer when dysregulated. In particular, pseudogene transcripts can function as competing endogenous RNAs (ceRNAs). The high similarity of gene and pseudogene nucleotide sequence has hindered experimental investigation of these mechanisms using RNA-seq. Furthermore, previous studies of pseudogenes in breast...

article

Deep Sequencing Shows Multiple Oligouridylations Are Required for 3′ to 5′ Degradation of Histone mRNAs on Polyribosomes

Michael K. Slevin, Stacie Meaux, Joshua D. Welch, Rebecca Bigler, more

Molecular Cell > 2014 > 53 > 6 > 1020-1030

Histone mRNAs are rapidly degraded when DNA replication is inhibited during S phase with degradation initiating with oligouridylation of the stem loop at the 3′ end. We developed a customized RNA sequencing strategy to identify the 3′ termini of degradation intermediates of histone mRNAs. Using this strategy, we identified two types of oligouridylated degradation intermediates: RNAs ending at different...

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INFONA - science communication portal

Search results for: Joshua D. Welch

Intercellular Interactions of an Adipogenic CXCL12‐Expressing Stromal Cell Subset in Murine Bone Marrow

MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data

Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

Deep Sequencing Shows Multiple Oligouridylations Are Required for 3′ to 5′ Degradation of Histone mRNAs on Polyribosomes

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INFONA - science communication portal

Search results for: Joshua D. Welch

Intercellular Interactions of an Adipogenic CXCL12‐Expressing Stromal Cell Subset in Murine Bone Marrow

MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data

Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

Deep Sequencing Shows Multiple Oligouridylations Are Required for 3′ to 5′ Degradation of Histone mRNAs on Polyribosomes

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