List of works - Theodore J. Perkins

A fluctuation method to quantify in vivo fluorescence data

scientific article

A general model of codon bias due to GC mutational bias

scientific article

A scaling law for random walks on networks.

scientific article

A trade-off between sample complexity and computational complexity in learning Boolean networks from time-series data

scientific article

Accuracy and reproducibility of somatic point mutation calling in clinical-type targeted sequencing data

scientific article published on 15 October 2020

Adaptive bandwidth kernel density estimation for next-generation sequencing data

scientific article

BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates.

scientific article

Bayesian Correlation Analysis for Sequence Count Data

scientific article (publication date: 2016)

Bayesian correlation is a robust gene similarity measure for single-cell RNA-seq data

scientific article published on 24 January 2020

Chromatin tandem affinity purification sequencing.

scientific article

Control of glioblastoma tumorigenesis by feed-forward cytokine signaling.

scientific article published on 25 April 2016

Correction: Estimating the Stochastic Bifurcation Structure of Cellular Networks.

scientific article published on 15 March 2010

Dynamical properties of model gene networks and implications for the inverse problem

scientific article published on 28 December 2005

Dynamics in Epistasis Analysis

scientific article published on 16 January 2017

Estimating the stochastic bifurcation structure of cellular networks

scientific article

FiloDetect: automatic detection of filopodia from fluorescence microscopy images

scientific article

Functional data analysis for identifying nonlinear models of gene regulatory networks

scientific article

Gene selection for the reconstruction of stem cell differentiation trees: a linear programming approach

scientific article published on 5 April 2015

Implementing arithmetic and other analytic operations by transcriptional regulation

scientific article

Induction of Activating Transcription Factor 3 Is Associated with Cisplatin Responsiveness in Non-Small Cell Lung Carcinoma Cells

scientific article published on September 2016

Inferring models of gene expression dynamics

scientific article published in October 2004

Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network

scientific article

Learning a cost function for microscope image segmentation

scientific article published on January 2014

MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data

scientific article

Maximum probability reaction sequences in stochastic chemical kinetic systems

scientific article

Methods for Determining the Statistical Significance of Enrichment or Depletion of Gene Ontology Classifications under Weighted Membership

scientific article published on 23 February 2012

Neural population densities shape network correlations

scientific article published on 17 February 2012

Noisy information processing through transcriptional regulation

scholarly article

On cross-conditional and fluctuation correlations in competitive RNA networks

scientific article published in September 2016

Pooled screening for synergistic interactions subject to blocking and noise

scientific article (publication date: 2014)

Quantitative epistasis analysis and pathway inference from genetic interaction data

scientific article

RECAP reveals the true statistical significance of ChIP-seq peak calls

scientific article published on 01 October 2019

Reverse engineering the gap gene network of Drosophila melanogaster

scientific article

Robust dynamics in minimal hybrid models of genetic networks

scientific article published on November 2010

Robust patterns in the stochastic organization of filopodia

scientific article

Statistical lower bounds on protein copy number from fluorescence expression images

scientific article published on 2 July 2009

Strategies for cellular decision-making

scientific article

Systematic discovery of Rab GTPases with synaptic functions in Drosophila

scientific article

The gap gene system of Drosophila melanogaster: model-fitting and validation

scientific article published on 12 October 2007

Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs

scientific article

Transcriptional reprogramming of skeletal muscle stem cells by the niche environment

scientific article published in 2023

Trichostatin A enhances vascular repair by injected human endothelial progenitors through increasing the expression of TAL1-dependent genes.

scientific article published in May 2014

UTX inhibition as selective epigenetic therapy against TAL1-driven T-cell acute lymphoblastic leukemia

scientific article published on March 2016

Uncovering robust patterns of microRNA co-expression across cancers using Bayesian Relevance Networks

scientific article

What do molecules do when we are not looking? State sequence analysis for stochastic chemical systems

scientific article published on 12 September 2012

miR Profiling Identifies Cyclin-Dependent Kinase 6 Downregulation as a Potential Mechanism of Acquired Cisplatin Resistance in Non-Small-Cell Lung Carcinoma

scientific article

List of works by Theodore J. Perkins

A fluctuation method to quantify in vivo fluorescence data

A general model of codon bias due to GC mutational bias

A scaling law for random walks on networks.

A trade-off between sample complexity and computational complexity in learning Boolean networks from time-series data

Accuracy and reproducibility of somatic point mutation calling in clinical-type targeted sequencing data

Adaptive bandwidth kernel density estimation for next-generation sequencing data

BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates.

Bayesian Correlation Analysis for Sequence Count Data

Bayesian correlation is a robust gene similarity measure for single-cell RNA-seq data

Chromatin tandem affinity purification sequencing.

Control of glioblastoma tumorigenesis by feed-forward cytokine signaling.

Correction: Estimating the Stochastic Bifurcation Structure of Cellular Networks.

Dynamical properties of model gene networks and implications for the inverse problem

Dynamics in Epistasis Analysis

Estimating the stochastic bifurcation structure of cellular networks

FiloDetect: automatic detection of filopodia from fluorescence microscopy images

Functional data analysis for identifying nonlinear models of gene regulatory networks

Gene selection for the reconstruction of stem cell differentiation trees: a linear programming approach

Implementing arithmetic and other analytic operations by transcriptional regulation

Induction of Activating Transcription Factor 3 Is Associated with Cisplatin Responsiveness in Non-Small Cell Lung Carcinoma Cells

Inferring models of gene expression dynamics

Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network

Learning a cost function for microscope image segmentation

MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data

Maximum probability reaction sequences in stochastic chemical kinetic systems

Methods for Determining the Statistical Significance of Enrichment or Depletion of Gene Ontology Classifications under Weighted Membership

Neural population densities shape network correlations

Noisy information processing through transcriptional regulation

On cross-conditional and fluctuation correlations in competitive RNA networks

Pooled screening for synergistic interactions subject to blocking and noise

Quantitative epistasis analysis and pathway inference from genetic interaction data

RECAP reveals the true statistical significance of ChIP-seq peak calls

Reverse engineering the gap gene network of Drosophila melanogaster

Robust dynamics in minimal hybrid models of genetic networks

Robust patterns in the stochastic organization of filopodia

Statistical lower bounds on protein copy number from fluorescence expression images

Strategies for cellular decision-making

Systematic discovery of Rab GTPases with synaptic functions in Drosophila

The gap gene system of Drosophila melanogaster: model-fitting and validation

Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs

Transcriptional reprogramming of skeletal muscle stem cells by the niche environment

Trichostatin A enhances vascular repair by injected human endothelial progenitors through increasing the expression of TAL1-dependent genes.

UTX inhibition as selective epigenetic therapy against TAL1-driven T-cell acute lymphoblastic leukemia

Uncovering robust patterns of microRNA co-expression across cancers using Bayesian Relevance Networks

What do molecules do when we are not looking? State sequence analysis for stochastic chemical systems

miR Profiling Identifies Cyclin-Dependent Kinase 6 Downregulation as a Potential Mechanism of Acquired Cisplatin Resistance in Non-Small-Cell Lung Carcinoma