Kenneth Daily
A5054638814- Polyomavirus and related diseases
- Genomics and Rare Diseases
- Genomic variations and chromosomal abnormalities
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- Single-cell and spatial transcriptomics
- Plant Virus Research Studies
- Bacteriophages and microbial interactions
- Computational Drug Discovery Methods
- Gene expression and cancer classification
- Pluripotent Stem Cells Research
- Antenna Design and Analysis
- CRISPR and Genetic Engineering
- Algorithms and Data Compression
- Chromosomal and Genetic Variations
- Genetic Associations and Epidemiology
- Advanced Vision and Imaging
- Epigenetics and DNA Methylation
- Cancer-related gene regulation
- Hedgehog Signaling Pathway Studies
- Metabolomics and Mass Spectrometry Studies
- Full-Duplex Wireless Communications
- Genomics and Phylogenetic Studies
- BRCA gene mutations in cancer
- Plant Disease Resistance and Genetics
National Institutes of Health
2014-2024
National Institute of Arthritis and Musculoskeletal and Skin Diseases
2024
Sage Bionetworks
2016-2023
University of Michigan
2017
National Cancer Institute
2014-2017
Center for Cancer Research
2015
University of California, Irvine
2010-2012
Indiana University Bloomington
2005
Abstract Background A central challenge of biology is to map and understand gene regulation on a genome-wide scale. For any given genome, only small fraction the regulatory elements embedded in DNA sequence have been characterized, there great interest developing computational methods systematically all these their relationships. Such efforts, however, are significantly hindered by overwhelming size non-coding regions statistical variability complex spatial organizations interactions....
The rigorous characterization of distinct induced pluripotent stem cells (iPSC) derived from multiple reprogramming technologies, somatic sources, and donors is required to understand potential sources variability downstream potential. To achieve this goal, the Progenitor Cell Biology Consortium performed comprehensive experimental genomic analyses 58 iPSC ten laboratories generated using a variety genes, vectors, cells. Associated global molecular studies identified functionally informative...
Abstract Motivation: The performance of classifiers is often assessed using Receiver Operating Characteristic ROC [or (AC) accumulation curve or enrichment curve] curves and the corresponding areas under (AUCs). However, in many fundamental problems ranging from information retrieval to drug discovery, only very top ranked list predictions any interest ROCs AUCs are not useful. New metrics, visualizations optimization tools needed address this ‘early retrieval’ problem. Results: To early...
The antagonistic actions of Polycomb and Trithorax are responsible for proper cell fate determination in mammalian tissues. In the epidermis, a self-renewing epithelium, previous work has shown that release from repression only partially explains differentiation gene activation. We now show is also key regulator epidermal differentiation, not through activation genes repressed by progenitor cells, but independent regulation Polycomb. associated transcription factor GRHL3/GET1 recruits...
The use of induced pluripotent stem cells (iPSC) derived from independent patients and sources holds considerable promise to improve the understanding development disease. However, optimized iPSC depends on our ability develop methods efficiently qualify cell lines protocols, monitor genetic stability, evaluate self-renewal differentiation potential. To accomplish these goals, 57 10 laboratories were differentiated 7 different states, resulting in 248 analyzed samples. Cell characterized at...
Abstract Background Post-zygotic mutations incurred during DNA replication, repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in from non-cancerous tissues poses significant challenges, particularly if the only are present a small fraction cells. Results Here, Brain Mosaicism Network conducts coordinated, multi-institutional study examine ability existing methods...
Abstract The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, matrix proteins. While these signals are normally tightly controlled, their dysregulation leads to phenotypic states associated with diverse diseases. To develop detailed understanding the linkage between changes, we generated comprehensive dataset that catalogs transcriptional, proteomic, epigenomic responses MCF10A mammary epithelial cells...
Abstract Background High-throughput sequencing (HTS) technologies play important roles in the life sciences by allowing rapid parallel of very large numbers relatively short nucleotide sequences, applications ranging from genome and resequencing to digital microarrays ChIP-Seq experiments. As experiments scale up, HTS create new bioinformatics challenges for storage sharing data. Results We develop data structures compression algorithms A processing stage maps sequences a reference or table...
// Maria Rita Gaiser 1 , Kenneth Daily 2 Jochen Hoffmann Maik Brune 3 Alexander Enk Isaac Brownell Department of Dermatology, University Heidelberg, Germany Dermatology Branch, Center for Cancer Research, National Institute, Institutes Health, Bethesda, MD, USA Internal Medicine I and Clinical Chemistry, Correspondence to: Gaiser, e-mail: maria-gaiser@gmx.de Keywords: Merkel cell carcinoma, neuron specific enolase, chromogranin A, circulating tumor cells, EpCAM Received: May 13, 2015...
Merkel cell carcinoma (MCC) and small lung cancer (SCLC) can be histologically similar. Immunohistochemistry (IHC) for cytokeratin 20 (CK20) thyroid transcription factor 1 (TTF-1) are commonly used to differentiate MCC from SCLC; however, these markers have limited sensitivity specificity. To identify new diagnostic markers, we performed differential gene expression analysis on transcriptome data SCLC tumors. Candidate included atonal BHLH (ATOH1) AP-2β (TFAP2B) MCC, as well carcinoembryonic...
Post-translational prote in modifications play an important role many protein path ways and interactions. It has been hypothesized that to insoccur regions are easily accessible, have determined belocated with intrinsically disordered regions. However, identifying precise locations of involve sex pensive time consuming laboratory work. Thus, automated identification these sites is helpful. This paper studies methylated proteins describes methods building a predictor for arginine lysine...
Although retroviruses are relatively promiscuous in choice of integration sites, retrotransposons can display marked specificity. In yeast and slime mold, some associated with tRNA genes (tDNAs). the Saccharomyces cerevisiae genome, long terminal repeat retrotransposon Ty3 is found at RNA polymerase III (Pol III) transcription start sites tDNAs. Ty1, 2, 4 elements also cluster upstream regions these genes. To determine extent to which other Pol III–transcribed serve as genomic targets for...
Late onset Alzheimer's disease is currently a with no known effective treatment options. To better understand disease, new multi-omic data-sets have recently been generated the goal of identifying molecular causes disease. However, most analytic studies using these datasets focus on uni-modal analysis data. Here, we propose data driven approach to integrate multiple types and outcomes aggregate evidences support hypothesis that gene genetic driver The main algorithmic contributions our...
Abstract Background New therapies for treating Alzheimer’s Disease (AD) are urgently needed. Discovery‐based research approaches have identified a host of promising new AD targets across spectrum therapeutic hypotheses. However, progress to validate selected and develop experimental reagents therapeutics requires efforts beyond the focus any single group. We built Agora site as an open repository that publicly shares information about facilitate target evaluation by broader community. Method...
Abstract Somatic mosaicism is defined as an occurrence of two or more populations cells having genomic sequences differing at given loci in individual who derived from a single zygote. It characteristic multicellular organisms that plays crucial role normal development and disease. To study the nature extent somatic autism spectrum disorder, bipolar focal cortical dysplasia, schizophrenia, Tourette syndrome, multi-institutional consortium called Brain Mosaicism Network (BSMN) was formed...
Abstract Post-zygotic mutations incurred during DNA replication, repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in from non-cancerous tissues poses significant challenges, particularly if the only are present a small fraction cells. Here, Brain Mosaicism Network conducted coordinated, multi-institutional study to: (i) examine ability existing methods detect...
SUMMARY The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, matrix. While these signals are normally tightly controlled, their dysregulation leads to phenotypic states associated with diverse diseases. To develop detailed understanding the linkage between changes, we generated comprehensive dataset that catalogs transcriptional, proteomic, epigenomic responses MCF10A mammary epithelial cells after...
ABSTRACT Motivation Late onset Alzheimers disease (LOAD) is currently a with no known effective treatment options. To address this, there have been recent surge in the generation of multi-modality data (Hodes and Buckholtz, 2016; Mueller et al ., 2005) to understand biology potential drivers that causally regulate it. However, most analytic studies using these data-sets focus on uni-modal analysis data. Here we propose data-driven approach integrate multiple types outcomes aggregate...
Live-cell imaging is an important technique to study cell migration and proliferation as well image-based profiling of drug perturbations over time. To gain biological insights from live-cell data, it necessary identify individual cells, follow them time extract quantitative information. However, since often experiment does not allow the high temporal resolution reduce excessive levels illumination or minimize unnecessary oversampling monitor long-term dynamics, still a challenging task...