Search Results to William Evan Johnson, PhD

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One or more keywords matched the following properties of Johnson, William

Research Expertise & Professional Interests William Johnson specializes in computational biology and biostatistics, developing new tools to investigate disease prognoses and causes and to help determine effective regimens based on individual patients’ risk factors. He has published in the journals Cell, Proceedings of the National Academy of Sciences, Biometrics, Nature Reviews Genetics, Annals of Applied Statistics, and Biostatistics. His work has been funded by the NIH. The focus of his group's research is to develop computational and statistical tools to investigate core components that contribute to disease prognosis and etiology, and for the accurate determination of optimal diagnostic, prognostic, and therapeutic regimens for individual patients. They are actively developing methods and software tools for data preprocessing, integration, and downstream analysis, and applying these tools in a variety of clinical and biomedical applications. Their work includes a balance between statistical methods development, algorithm optimization, and clinical application. Statistical innovation focuses on the development of clinically motivated tools that integrate linear modeling, Bayesian methods, factor analysis and structural equations models, Hidden Markov models, mixture models, dynamic programming, and high-performance parallel computing. This work has resulted in widely used tools and algorithms for profiling transcription factors (MAT, MA2C), preprocessing and integrating of genomic data (ComBat, BatchQC, SCAN-UPC), aligning sequencing reads (GNUMAP), developing multi-gene biomarker signatures (ASSIGN), and metagenomic profiling (PathoScope). They have successfully applied their tools in several biomedical and clinical scenarios, ranging from mechanistic studies and to precision genomics.
Self-Described Keywords Bayesian biostatistics
Self-Described Keywords Computational biology

One or more keywords matched the following items that are connected to Johnson, William

Item TypeName
Concept Algorithms
Concept Chromatography, Liquid
Concept Chromosome Mapping
Concept Computer Simulation
Concept Immunosuppression
Concept Lymphocyte Activation
Concept Microbiological Techniques
Concept Models, Theoretical
Concept Pain Measurement
Concept Peer Review
Concept Psychiatric Status Rating Scales
Concept Research Design
Concept Statistics as Topic
Concept User-Computer Interface
Concept Cohort Studies
Concept Case-Control Studies
Concept Polymerase Chain Reaction
Concept Sequence Alignment
Concept Sequence Analysis
Concept Sequence Analysis, DNA
Concept Sequence Analysis, RNA
Concept Computational Biology
Concept Amino Acid Substitution
Concept Oligonucleotide Array Sequence Analysis
Concept Two-Hybrid System Techniques
Concept Gene Expression Profiling
Concept Microarray Analysis
Concept Chromatin Immunoprecipitation
Concept Tandem Mass Spectrometry
Concept Genome-Wide Association Study
Concept High-Throughput Screening Assays
Concept DNA Barcoding, Taxonomic
Concept Molecular Sequence Annotation
Concept High-Throughput Nucleotide Sequencing
Academic Article Adjusting batch effects in microarray expression data using empirical Bayes methods.
Academic Article Model-based analysis of tiling-arrays for ChIP-chip.
Academic Article Model-based analysis of two-color arrays (MA2C).
Academic Article A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments.
Academic Article The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing.
Academic Article Tackling the widespread and critical impact of batch effects in high-throughput data.
Academic Article Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer.
Academic Article Dynamic linear model for the identification of miRNAs in next-generation sequencing data.
Academic Article A pharmacogenomic method for individualized prediction of drug sensitivity.
Academic Article A single-sample microarray normalization method to facilitate personalized-medicine workflows.
Academic Article Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data.
Academic Article PathoQC: Computationally Efficient Read Preprocessing and Quality Control for High-Throughput Sequencing Data Sets.
Academic Article Pathoscope: species identification and strain attribution with unassembled sequencing data.
Academic Article Multiplatform single-sample estimates of transcriptional activation.
Academic Article PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples.
Academic Article Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data.
Academic Article Concordance and discordance of sequence survey methods for molecular epidemiology.
Academic Article Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.
Academic Article BatchQC: interactive software for evaluating sample and batch effects in genomic data.

Search Criteria
  • Bayesian
  • Methods
  • Computing
  • Algorithms