Search results for: Charles C. Kim

Items from 1 to 12 out of 12 results

article

Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance

Alyssa Baccarella, Claire R. Williams, Jay Z. Parrish, Charles C. Kim

BMC Bioinformatics > 2018 > 19 > 1 > 1-12

Background RNA-Sequencing analysis methods are rapidly evolving, and the tool choice for each step of one common workflow, differential expression analysis, which includes read alignment, expression modeling, and differentially expressed gene identification, has a dramatic impact on performance characteristics. Although a number of workflows are emerging as high performers that are robust to diverse...

article

Ret and Substrate-Derived TGF-β Maverick Regulate Space-Filling Dendrite Growth in Drosophila Sensory Neurons

Nina Hoyer, Philip Zielke, Chun Hu, Meike Petersen, more

Cell Reports > 2018 > 24 > 9 > 2261-2272.e5

Dendrite morphogenesis is a highly regulated process that gives rise to stereotyped receptive fields, which are required for proper neuronal connectivity and function. Specific classes of neurons, including Drosophila class IV dendritic arborization (C4da) neurons, also feature complete space-filling growth of dendrites. In this system, we have identified the substrate-derived TGF-β ligand maverick...

article

Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq

Claire R. Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim

BMC Bioinformatics > 2017 > 18 > 1 > 1-12

Background RNA-Seq has supplanted microarrays as the preferred method of transcriptome-wide identification of differentially expressed genes. However, RNA-Seq analysis is still rapidly evolving, with a large number of tools available for each of the three major processing steps: read alignment, expression modeling, and identification of differentially expressed genes. Although some studies have benchmarked...

article

Progranulin Deficiency Promotes Circuit-Specific Synaptic Pruning by Microglia via Complement Activation

Hansen Lui, Jiasheng Zhang, Stefanie R. Makinson, Michelle K. Cahill, more

Cell > 2016 > 165 > 4 > 921-935

Microglia maintain homeostasis in the brain, but whether aberrant microglial activation can cause neurodegeneration remains controversial. Here, we use transcriptome profiling to demonstrate that deficiency in frontotemporal dementia (FTD) gene progranulin (Grn) leads to an age-dependent, progressive upregulation of lysosomal and innate immunity genes, increased complement production, and enhanced...

article

Saturated Fatty Acids Engage an IRE1α-Dependent Pathway to Activate the NLRP3 Inflammasome in Myeloid Cells

Megan M. Robblee, Charles C. Kim, Jess Porter Abate, Martin Valdearcos, more

Cell Reports > 2016 > 14 > 11 > 2611-2623

Diets rich in saturated fatty acids (SFAs) produce a form of tissue inflammation driven by “metabolically activated” macrophages. We show that SFAs, when in excess, induce a unique transcriptional signature in both mouse and human macrophages that is enriched by a subset of ER stress markers, particularly IRE1α and many adaptive downstream target genes. SFAs also activate the NLRP3 inflammasome in...

article

Brain trauma elicits non-canonical macrophage activation states

Charles C. Kim, Mary C. Nakamura, Christine L. Hsieh

Journal of Neuroinflammation > 2016 > 13 > 1 > 1-12

Background Macrophage polarization programs, commonly referred to as “classical” and “alternative” activation, are widely considered as distinct states that are exclusive of one another and are associated with different functions such as inflammation and wound healing, respectively. In a number of disease contexts, such as traumatic brain injury (TBI), macrophage polarization influences the extent...

article

Trimming of sequence reads alters RNA-Seq gene expression estimates

Claire R. Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim

BMC Bioinformatics > 2016 > 17 > 1 > 1-13

Background High-throughput RNA-Sequencing (RNA-Seq) has become the preferred technique for studying gene expression differences between biological samples and for discovering novel isoforms, though the techniques to analyze the resulting data are still immature. One pre-processing step that is widely but heterogeneously applied is trimming, in which low quality bases, identified by the probability...

article

Beyond the transcriptome: completion of act one of the Immunological Genome Project

Charles C Kim, Lewis L Lanier

Current Opinion in Immunology > 2013 > 25 > 5 > 593-597

The Immunological Genome Consortium has generated a public resource (www.immgen.org) that provides a compendium of gene expression profiles of ∼270 leukocyte subsets in the mouse. This effort established carefully standardized operating procedures that resulted in a transcriptional dataset of unprecedented comprehensiveness and quality. The findings have been detailed recently in a series of publications...

article

Traumatic brain injury induces macrophage subsets in the brain

Christine L. Hsieh, Charles C. Kim, Bryan E. Ryba, Erene C. Niemi, more

European Journal of Immunology > 43 > 8 > 2010 - 2022

Traumatic brain injury (TBI) elicits innate inflammatory responses that can lead to secondary brain injury. To better understand the mechanisms involved in TBI‐induced inflammation, we examined the nature of macrophages responding to TBI in mice. In this model, brain macrophages were increased >20‐fold the day after injury and >77‐fold 4 days after injury in the ipsilateral hemisphere compared...

article

The microRNA bantam Functions in Epithelial Cells to Regulate Scaling Growth of Dendrite Arbors in Drosophila Sensory Neurons

Jay Z. Parrish, Peizhang Xu, Charles C. Kim, Lily Yeh Jan, more

Neuron > 2009 > 63 > 6 > 788-802

In addition to establishing dendritic coverage of the receptive field, neurons need to adjust their dendritic arbors to match changes of the receptive field. Here, we show that dendrite arborization (da) sensory neurons establish dendritic coverage of the body wall early in Drosophila larval development and then grow in precise proportion to their substrate, the underlying body wall epithelium, as...

article

Temperature dependence of the optical properties of Hg_1−xCd_xTe

Charles C. Kim, S. Sivananthan

Journal of Electronic Materials > 1997 > 26 > 6 > 561-566

The alloy composition of Hg_1−xCd_xTe should be controlled during growth, so that the desired band gap and the lattice-matched layer may be obtained. In-situ spectroscopic ellipsometry, now commercially available, enables one to acquire spectral data during growth. If one knows the optical dielectric function as a function of alloy composition and temperature, the technique can be fully used to monitor...

article

Vibrational analysis of beryl (Be ₃ Al ₂ Si ₆ O ₁ ₈ ) and its constituent ring (Si ₆ O ₁ ₈ )

Charles C. Kim, M.I. Bell, D.A. McKeown

Physica B: Physics of Condensed Matter > 1995 > 205 > 2 > 193-208

The normal modes of vibration and their frequencies are calculated for beryl, a mineral whose crystal structure (space group D ² ₆ _h ) consists of six-membered silicate rings (Si ₆ O ₁ ₈ ) linked by Be ² ⁺ and Al ³ ⁺ ions. A valence force potential is used, consisting of central interactions between nearest neighbors and bond-bending interactions...

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