List of works - Frank Emmert-Streib

2-(2-(2,4-dioxopentan-3-ylidene)hydrazineyl)benzonitrile as novel inhibitor of receptor tyrosine kinase and PI3K/AKT/mTOR signaling pathway in glioblastoma

scientific article published on 22 January 2019

A BRCA1 deficient, NFκB driven immune signal predicts good outcome in triple negative breast cancer

scientific article published on 02 March 2016

A Bayesian analysis of the chromosome architecture of human disorders by integrating reductionist data

scientific article

A Graph Theoretic Approach to Construct Desired Cryptographic Boolean Functions

scholarly article

A Note on Graphs with Prescribed Orbit Structure ⬇️

scholarly article

A comprehensive survey of error measures for evaluating binary decision making in data science

scientific article published on 08 February 2019

A data-centric review of deep transfer learning with applications to text data

scientific article published on 27 November 2021

A review of connectivity map and computational approaches in pharmacogenomics

scientific article published on 01 September 2017

A review of connectivity map and computational approaches in pharmacogenomics.

scientific article

A topological algorithm for identification of structural domains of proteins.

scientific article

Against Dataism and for Data Sharing of Big Biomedical and Clinical Data with Research Parasites

scientific article

Algorithmic computation of knot polynomials of secondary structure elements of proteins.

scientific article

Alkylaminophenol Induces G1/S Phase Cell Cycle Arrest in Glioblastoma Cells Through p53 and Cyclin-Dependent Kinase Signaling Pathway

scientific article published on 02 April 2019

An Introductory Review of Deep Learning for Prediction Models With Big Data ⬇️

publication published on 28 February 2020

Analyzing the Scholarly Literature of Digital Twin Research: Trends, Topics and Structure

scientific article published in 2023

Assessment method for a power analysis to identify differentially expressed pathways

scientific article

B-cell lymphoma gene regulatory networks: biological consistency among inference methods.

scientific article published on 16 December 2013

Bagging statistical network inference from large-scale gene expression data

scientific article

Biological networks: the microscope of the twenty-first century?

scientific article published on 13 October 2015

Can ChatGPT understand genetics?

scientific article published in 2023

Collectives of diagnostic biomarkers identify high-risk subpopulations of hematuria patients: exploiting heterogeneity in large-scale biomarker data

scientific article

Combining deep learning with token selection for patient phenotyping from electronic health records

scientific article published on 29 January 2020

Comparative evaluation of gene set analysis approaches for RNA-Seq data.

scientific article

Comparing biological information contained in mRNA and non-coding RNAs for classification of lung cancer patients

scientific article published on 03 December 2019

Comparing deep belief networks with support vector machines for classifying gene expression data from complex disorders

article

Comparison of Text Mining Models for Food and Dietary Constituent Named-Entity Recognition

scientific article published in 2022

Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules.

scientific article

Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with potential for clinical utility.

scientific article

Computational cancer biology: education is a natural key to many locks

scientific article published on 15 January 2015

Connections between classical and parametric network entropies

scientific article (publication date: 5 January 2011)

CoopRA Algorithm for Universal Characterization of the Experimental Evaluation Results of Cooperative Multiagent Systems

Scientific article

Correction: Limitations of Gene Duplication Models: Evolution of Modules in Protein Interaction Networks.

scientific article published on 7 June 2012

Detecting sequence dependent transcriptional pauses from RNA and protein number time series.

scientific article

Discrimination Power of Polynomial-Based Descriptors for Graphs by Using Functional Matrices

scientific article published on 19 October 2015

Dry computational approaches for wet medical problems

scientific article published on 25 January 2014

Effects of subsampling on characteristics of RNA-seq data from triple-negative breast cancer patients

scientific article

Enhancing our understanding of ways to analyze metagenomes

scientific article

Enhancing systems medicine beyond genotype data by dynamic patient signatures: having information and using it too

scientific article

Ensuring Quality Standards and Reproducible Research for Data Analysis Services in Oncology: A Cooperative Service Model

scientific article published on 17 December 2019

Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential

scientific article published on 6 February 2013

Entropy bounds for hierarchical molecular networks

scientific article

Evaluation of Regression Models: Model Assessment, Model Selection and Generalization Error

scholarly article

Exploiting Genomic Relations in Big Data Repositories by Graph-Based Search Methods

scientific article published on 23 November 2018

Exploratory analysis of spatiotemporal patterns of cellular automata by clustering compressibility.

scientific article published on 8 February 2010

Exploring statistical and population aspects of network complexity

scientific article (publication date: 2012)

Extracting the Strongest Signals from Omics Data: Differentially Expressed Pathways and Beyond.

scientific article published on January 2017

Extracting the dynamics of perceptual switching from 'noisy' behaviour: an application of hidden Markov modelling to pecking data from pigeons.

scientific article

Functional and genetic analysis of the colon cancer network

scientific article

GSAR: Bioconductor package for Gene Set analysis in R

scientific article

Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets.

scientific article published on 30 November 2013

Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks

scientific article published on 19 August 2014

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline

scientific article

Gene set analysis for self-contained tests: complex null and specific alternative hypotheses

scientific article published on 7 October 2012

Glioblastoma Multiforme Stem Cell Cycle Arrest by Alkylaminophenol Through the Modulation of EGFR and CSC Signaling Pathways

scientific article published on 10 March 2020

Global Genetics Research in Prostate Cancer: A Text Mining and Computational Network Theory Approach

article

Graph entropy based on the number of spanning forests of c-cyclic graphs

scholarly article

Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance

scientific article published on 07 October 2020

Harnessing naturally randomized transcription to infer regulatory relationships among genes

scientific article (publication date: 2007)

Harnessing the biological complexity of Big Data from LINCS gene expression signatures

scientific article published in PLoS ONE

Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods

scientific article

Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae

scientific article published on 20 July 2009

Human Team Behavior and Predictability in the Massively Multiplayer Online Game WOT Blitz

scientific article published on 26 August 2023

Impact of Variable RNA-Sequencing Depth on Gene Expression Signatures and Target Compound Robustness: Case Study Examining Brain Tumor (Glioma) Disease Progression

article

Inference and validation of predictive gene networks from biomedical literature and gene expression data

scientific article

Inferring the conservative causal core of gene regulatory networks

scientific article

Influence of statistical estimators of mutual information and data heterogeneity on the inference of gene regulatory networks

scientific article

Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors.

scientific article

Influence of the time scale on the construction of financial networks

scientific article

Information fusion as an integrative cross-cutting enabler to achieve robust, explainable, and trustworthy medical artificial intelligence

scientific article published in 2022

Information processing in the transcriptional regulatory network of yeast: functional robustness

scientific article

Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information

scientific article

Interrelations of graph distance measures based on topological indices

scientific article (publication date: 2014)

Introduction to Survival Analysis in Practice

scholarly article

L1000 Viewer: A Search Engine and Web Interface for the LINCS Data Repository.

scientific article published on 14 June 2019

Large-Scale Simultaneous Inference with Hypothesis Testing: Multiple Testing Procedures in Practice

scholarly article

Large-scale evaluation of molecular descriptors by means of clustering

scientific article

Lessons from the Human Genome Project: Modesty, Honesty, and Realism.

scientific article published on 23 November 2017

Limitations of Gene Duplication Models: Evolution of Modules in Protein Interaction Networks ⬇️

scientific article published on April 18, 2012

Local network-based measures to assess the inferability of different regulatory networks.

scientific article published in July 2010

Measuring the complexity of directed graphs: A polynomial-based approach

scientific article published on 14 November 2019

MetrIntMeas a novel metric for measuring the intelligence of a swarm of cooperating agents

scientific article

MetrIntSimil-An Accurate and Robust Metric for Comparison of Similarity in Intelligence of Any Number of Cooperative Multiagent Systems

scientific article

Multilayer Aggregation with Statistical Validation: Application to Investor Networks. ⬇️

scientific article

Named Entity Recognition and Relation Detection for Biomedical Information Extraction

scientific article published on 28 August 2020

NetBioV: an R package for visualizing large network data in biology and medicine

scientific article

Netmes: assessing gene network inference algorithms by network-based measures

scientific article published on 6 February 2014

Network Science: From Chemistry to Digital Society

scholarly article

Network biology: a direct approach to study biological function

scientific article published on 31 December 2010

Network nursing: connections between nursing and complex network science

scientific article

Networks for systems biology: conceptual connection of data and function

scientific article

On Properties of Distance-Based Entropies on Fullerene Graphs

scientific article published on 10 May 2019

On entropy-based molecular descriptors: statistical analysis of real and synthetic chemical structures

scientific article published in July 2009

On graph entropy measures based on the number of independent sets and matchings ⬇️

scholarly article

Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma

scientific article

Parametric Construction of Episode Networks from Pseudoperiodic Time Series Based on Mutual Information ⬇️

scientific article published on December 22, 2011

Pathway analysis of expression data: deciphering functional building blocks of complex diseases

scientific article

Personalized medicine: Has it started yet? A reconstruction of the early history ⬇️

scientific article published on January 8, 2013

Predicting cell cycle regulated genes by causal interactions

scientific article

Prostate Cancer Gene Regulatory Network Inferred from RNA-Seq Data

article

Proteome-transcriptome alignment of molecular portraits achieved by self-contained gene set analysis: Consensus colon cancer subtypes case study

scientific article published on 22 August 2019

Quantitative assessment and validation of network inference methods in bioinformatics

scientific article published on 16 July 2014

Quantitative network measures as biomarkers for classifying prostate cancer disease states: a systems approach to diagnostic biomarkers

scientific article

Relevance of different prior knowledge sources for inferring gene interaction networks

scientific article published on 24 June 2014

Report from the 2nd Summer School in Computational Biology organized by the Queen's University of Belfast.

scientific article published on 13 February 2014

Revealing differences in gene network inference algorithms on the network level by ensemble methods.

scientific article

Robustness of differential gene expression analysis of RNA-seq

scientific article published on 26 May 2021

Standardization of diagnostic biomarker concentrations in urine: the hematuria caveat

scientific article

Statistic Complexity: Combining Kolmogorov Complexity with an Ensemble Approach ⬇️

scientific article published on August 26, 2010

Statistical inference and reverse engineering of gene regulatory networks from observational expression data

scientific article

Structural Analysis of Treatment Cycles Representing Transitions between Nursing Organizational Units Inferred from Diabetes

scientific article published on June 2015

Structural Properties and Complexity of a New Network Class: Collatz Step Graphs ⬇️

scientific article published on February 19, 2013

Structural influence of gene networks on their inference: analysis of C3NET.

scientific article published on 22 June 2011

Structural information content of networks: graph entropy based on local vertex functionals.

scientific article published on 29 September 2007

Structural measures for network biology using QuACN

scientific article published on 24 December 2011

Systems Pharmacogenomic Landscape of Drug Similarities from LINCS data: Drug Association Networks

scientific article published on 24 May 2019

Taxonomy of machine learning paradigms: A data‐centric perspective

scientific article published in 2022

The Hosoya Entropy of Graphs Revisited

scholarly article

The Need for Formally Defining "Modern Medicine" by Means of Experimental Design

scientific article published on 20 April 2016

The Process of Analyzing Data is the Emergent Feature of Data Science.

scientific article

The chronic fatigue syndrome: a comparative pathway analysis.

scientific article published on September 2007

The gene regulatory network for breast cancer: integrated regulatory landscape of cancer hallmarks

scientific article published on 03 February 2014

Understanding Statistical Hypothesis Testing: The Logic of Statistical Inference

scholarly article

Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets

scientific article published on 2 July 2009

Untangling statistical and biological models to understand network inference: the need for a genomics network ontology ⬇️

scientific article published on 29 August 2014

Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data

scientific article published on 14 May 2015

Using shRNA experiments to validate gene regulatory networks

scientific article

Utilizing Social Media Data for Psychoanalysis to Study Human Personality

scientific article published on 15 November 2019

[COMMODE] a large-scale database of molecular descriptors using compounds from PubChem

scientific article published on 13 November 2013

samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files.

scientific article published on 10 July 2016

sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters

scientific article

List of works by Frank Emmert-Streib

2-(2-(2,4-dioxopentan-3-ylidene)hydrazineyl)benzonitrile as novel inhibitor of receptor tyrosine kinase and PI3K/AKT/mTOR signaling pathway in glioblastoma

A BRCA1 deficient, NFκB driven immune signal predicts good outcome in triple negative breast cancer

A Bayesian analysis of the chromosome architecture of human disorders by integrating reductionist data

A Graph Theoretic Approach to Construct Desired Cryptographic Boolean Functions

A Note on Graphs with Prescribed Orbit Structure ⬇️

A comprehensive survey of error measures for evaluating binary decision making in data science

A data-centric review of deep transfer learning with applications to text data

A review of connectivity map and computational approaches in pharmacogenomics

A review of connectivity map and computational approaches in pharmacogenomics.

A topological algorithm for identification of structural domains of proteins.

Against Dataism and for Data Sharing of Big Biomedical and Clinical Data with Research Parasites

Algorithmic computation of knot polynomials of secondary structure elements of proteins.

Alkylaminophenol Induces G1/S Phase Cell Cycle Arrest in Glioblastoma Cells Through p53 and Cyclin-Dependent Kinase Signaling Pathway

An Introductory Review of Deep Learning for Prediction Models With Big Data ⬇️

Analyzing the Scholarly Literature of Digital Twin Research: Trends, Topics and Structure

Assessment method for a power analysis to identify differentially expressed pathways

B-cell lymphoma gene regulatory networks: biological consistency among inference methods.

Bagging statistical network inference from large-scale gene expression data

Biological networks: the microscope of the twenty-first century?

Can ChatGPT understand genetics?

Collectives of diagnostic biomarkers identify high-risk subpopulations of hematuria patients: exploiting heterogeneity in large-scale biomarker data

Combining deep learning with token selection for patient phenotyping from electronic health records

Comparative evaluation of gene set analysis approaches for RNA-Seq data.

Comparing biological information contained in mRNA and non-coding RNAs for classification of lung cancer patients

Comparing deep belief networks with support vector machines for classifying gene expression data from complex disorders

Comparison of Text Mining Models for Food and Dietary Constituent Named-Entity Recognition

Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules.

Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with potential for clinical utility.

Computational cancer biology: education is a natural key to many locks

Connections between classical and parametric network entropies

CoopRA Algorithm for Universal Characterization of the Experimental Evaluation Results of Cooperative Multiagent Systems

Correction: Limitations of Gene Duplication Models: Evolution of Modules in Protein Interaction Networks.

Detecting sequence dependent transcriptional pauses from RNA and protein number time series.

Discrimination Power of Polynomial-Based Descriptors for Graphs by Using Functional Matrices

Dry computational approaches for wet medical problems

Effects of subsampling on characteristics of RNA-seq data from triple-negative breast cancer patients

Enhancing our understanding of ways to analyze metagenomes

Enhancing systems medicine beyond genotype data by dynamic patient signatures: having information and using it too

Ensuring Quality Standards and Reproducible Research for Data Analysis Services in Oncology: A Cooperative Service Model

Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential

Entropy bounds for hierarchical molecular networks

Evaluation of Regression Models: Model Assessment, Model Selection and Generalization Error

Exploiting Genomic Relations in Big Data Repositories by Graph-Based Search Methods

Exploratory analysis of spatiotemporal patterns of cellular automata by clustering compressibility.

Exploring statistical and population aspects of network complexity

Extracting the Strongest Signals from Omics Data: Differentially Expressed Pathways and Beyond.

Extracting the dynamics of perceptual switching from 'noisy' behaviour: an application of hidden Markov modelling to pecking data from pigeons.

Functional and genetic analysis of the colon cancer network

GSAR: Bioconductor package for Gene Set analysis in R

Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets.

Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline

Gene set analysis for self-contained tests: complex null and specific alternative hypotheses

Glioblastoma Multiforme Stem Cell Cycle Arrest by Alkylaminophenol Through the Modulation of EGFR and CSC Signaling Pathways

Global Genetics Research in Prostate Cancer: A Text Mining and Computational Network Theory Approach

Graph entropy based on the number of spanning forests of c-cyclic graphs

Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance

Harnessing naturally randomized transcription to infer regulatory relationships among genes

Harnessing the biological complexity of Big Data from LINCS gene expression signatures

Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods

Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae

Human Team Behavior and Predictability in the Massively Multiplayer Online Game WOT Blitz

Impact of Variable RNA-Sequencing Depth on Gene Expression Signatures and Target Compound Robustness: Case Study Examining Brain Tumor (Glioma) Disease Progression

Inference and validation of predictive gene networks from biomedical literature and gene expression data

Inferring the conservative causal core of gene regulatory networks

Influence of statistical estimators of mutual information and data heterogeneity on the inference of gene regulatory networks

Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors.

Influence of the time scale on the construction of financial networks

Information fusion as an integrative cross-cutting enabler to achieve robust, explainable, and trustworthy medical artificial intelligence

Information processing in the transcriptional regulatory network of yeast: functional robustness

Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information

Interrelations of graph distance measures based on topological indices

Introduction to Survival Analysis in Practice

L1000 Viewer: A Search Engine and Web Interface for the LINCS Data Repository.

Large-Scale Simultaneous Inference with Hypothesis Testing: Multiple Testing Procedures in Practice

Large-scale evaluation of molecular descriptors by means of clustering

Lessons from the Human Genome Project: Modesty, Honesty, and Realism.

Limitations of Gene Duplication Models: Evolution of Modules in Protein Interaction Networks ⬇️

Local network-based measures to assess the inferability of different regulatory networks.