Information Theory in Computational Biology: Where We Stand Today

Asymptotic Distributions of Empirical Interaction Information

(2020) Mariusz Kubkowski et al.   METHODOLOGY AND COMPUTING IN APPLIED PROBABILITY

Long-Read Sequencing – A Powerful Tool in Viral Transcriptome Research

(2019) Zsolt Boldogkői et al.   TRENDS IN MICROBIOLOGY

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

Long-Read Sequencing Emerging in Medical Genetics

(2019) Tuomo Mantere et al.   Frontiers in Genetics

Measuring gene-gene interaction using Kullback-Leibler divergence

(2019) Guanjie Chen et al.   ANNALS OF HUMAN GENETICS

DNA assembly for nanopore data storage readout

(2019) Randolph Lopez et al.   Nature Communications

High information capacity DNA-based data storage with augmented encoding characters using degenerate bases

(2019) Yeongjae Choi et al.   Scientific Reports

A Unified Conceptual Framework for Metabolic Phenotyping in Diagnosis and Prognosis

(2019) Jeremy R. Everett et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Reading and writing digital data in DNA

(2019) Linda C. Meiser et al.   Nature Protocols

Past–future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics

(2019) Yihang Wang et al.   Nature Communications

Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data

(2018) Shuonan Chen et al.   BMC BIOINFORMATICS

Inter-residue, inter-protein and inter-family coevolution: bridging the scales

(2018) Hendrik Szurmant et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

From correlation to causation: analysis of metabolomics data using systems biology approaches

(2018) Antonio Rosato et al.   Metabolomics

RNentropy: an entropy-based tool for the detection of significant variation of gene expression across multiple RNA-Seq experiments

(2018) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation Using Maximum Entropy-Based Simulations with Application to Central Metabolism of Neurospora crassa

(2018) William Cannon et al.   Processes

Deep learning for biology

(2018) Sarah Webb   NATURE

Statistical mechanics for metabolic networks during steady state growth

(2018) Daniele De Martino et al.   Nature Communications

Use of Information Measures and Their Approximations to Detect Predictive Gene-Gene Interaction

(2017) Jan Mielniczuk et al.   Entropy

Information-Theoretic Analysis of Haplotype Assembly

(2017) Hongbo Si et al.   IEEE TRANSACTIONS ON INFORMATION THEORY

Highly accurate fluorogenic DNA sequencing with information theory–based error correction

(2017) Zitian Chen et al.   NATURE BIOTECHNOLOGY

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

(2017) Kazuma Nakano et al.   Human Cell

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity

(2017) Kevin D. Murray et al.   PLoS Computational Biology

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures

(2017) Thalia E. Chan et al.   Cell Systems

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information

(2016) Alexander Lachmann et al.   BIOINFORMATICS

Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons

(2016) Alexandre Drouin et al.   BMC GENOMICS

Transferring entropy to the realm of GxG interactions

(2016) Paola G. Ferrario et al.   BRIEFINGS IN BIOINFORMATICS

A Critical Look at Entropy-Based Gene-Gene Interaction Measures

(2016) Woojoo Lee et al.   GENETIC EPIDEMIOLOGY

Entropy-Based Network Representation of the Individual Metabolic Phenotype

(2016) Edoardo Saccenti et al.   JOURNAL OF PROTEOME RESEARCH

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

Transition states and cell fate decisions in epigenetic landscapes

(2016) Naomi Moris et al.   NATURE REVIEWS GENETICS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Techniques for the analysis of protein-protein interactions in vivo

(2016) Shuping Xing et al.   PLANT PHYSIOLOGY

Estimating evolutionary distances between genomic sequences from spaced-word matches

(2015) Burkhard Morgenstern et al.   Algorithms for Molecular Biology

CoGI: Towards Compressing Genomes as an Image

(2015) Xiaojing Xie et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Higher-order genetic interactions and their contribution to complex traits

(2015) Matthew B. Taylor et al.   TRENDS IN GENETICS

Detecting Genetic Interactions for Quantitative Traits Usingm-Spacing Entropy Measure

(2015) Jaeyong Yee et al.   Biomed Research International

A multi-tissue genome-scale metabolic modeling framework for the analysis of whole plant systems

(2015) Cristiana Gomes de Oliveira Dal'Molin et al.   Frontiers in Plant Science

Entropy-Scaling Search of Massive Biological Data

(2015) Y. William Yu et al.   Cell Systems

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

iDoComp: a compression scheme for assembled genomes

(2014) Idoia Ochoa et al.   BIOINFORMATICS

Fast alignment-free sequence comparison using spaced-word frequencies

(2014) Chris-Andre Leimeister et al.   BIOINFORMATICS

An overview of SNP interactions in genome-wide association studies

(2014) P. Li et al.   Briefings in Functional Genomics

Big Data Bioinformatics

(2014) Casey S. Greene et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Comparison of Optimal Thermodynamic Models of the Tricarboxylic Acid Cycle from Heterotrophs, Cyanobacteria, and Green Sulfur Bacteria

(2014) Dennis G. Thomas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Probabilistic Networks of Blood Metabolites in Healthy Subjects As Indicators of Latent Cardiovascular Risk

(2014) Edoardo Saccenti et al.   JOURNAL OF PROTEOME RESEARCH

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Comparison of Metatranscriptomic Samples Based on k-Tuple Frequencies

(2014) Ying Wang et al.   PLoS One

Simulating Metabolism with Statistical Thermodynamics

(2014) William R. Cannon   PLoS One

These Are Not the K-mers You Are Looking For: Efficient Online K-mer Counting Using a Probabilistic Data Structure

(2014) Qingpeng Zhang et al.   PLoS One

Noise in biology

(2014) Lev S Tsimring   REPORTS ON PROGRESS IN PHYSICS

Multiple hypothesis testing in genomics

(2014) Jelle J. Goeman et al.   STATISTICS IN MEDICINE

The role of protein interaction networks in systems biomedicine

(2014) Tuba Sevimoglu et al.   Computational and Structural Biotechnology Journal

Sequence analysis by iterated maps, a review

(2013) J. S. Almeida   BRIEFINGS IN BIOINFORMATICS

Information theory applications for biological sequence analysis

(2013) S. Vinga   BRIEFINGS IN BIOINFORMATICS

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis

(2013) O. Bonham-Carter et al.   BRIEFINGS IN BIOINFORMATICS

EpiMiner: A three-stage co-information based method for detecting and visualizing epistatic interactions

(2013) Junliang Shang et al.   DIGITAL SIGNAL PROCESSING

ViSEN: Methodology and Software for Visualization of Statistical Epistasis Networks

(2013) Ting Hu et al.   GENETIC EPIDEMIOLOGY

SYMPHONY, an information-theoretic method for gene–gene and gene–environment interaction analysis of disease syndromes

(2013) J Knights et al.   HEREDITY

Information Theory of DNA Shotgun Sequencing

(2013) Abolfazl S. Motahari et al.   IEEE TRANSACTIONS ON INFORMATION THEORY

An information-gain approach to detecting three-way epistatic interactions in genetic association studies

(2013) Ting Hu et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

A Modified Entropy-Based Approach for Identifying Gene-Gene Interactions in Case-Control Study

(2013) Jaeyong Yee et al.   PLoS One

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests

(2013) I. S. Jang et al.   Interface Focus

Genetic Association Studies: An Information Content Perspective

(2012) Cen Wu et al.   CURRENT GENOMICS

An Information Theory Analysis of Gene-Environmental Interactions in Count/Rate Data

(2012) Jonathan Knights et al.   HUMAN HEREDITY

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

History of protein-protein interactions: From egg-white to complex networks

(2012) Pascal Braun et al.   PROTEOMICS

Noise in cellular signaling pathways: causes and effects

(2012) John E. Ladbury et al.   TRENDS IN BIOCHEMICAL SCIENCES

Information theory based approaches to cellular signaling

(2011) Christian Waltermann et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

An empirical comparison of several recent epistatic interaction detection methods

(2011) Y. Wang et al.   BIOINFORMATICS

Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information

(2011) Xiujun Zhang et al.   BIOINFORMATICS

Characterizing genetic interactions in human disease association studies using statistical epistasis networks

(2011) Ting Hu et al.   BMC BIOINFORMATICS

Comparative analysis of methods for detecting interacting loci

(2011) Li Chen et al.   BMC GENOMICS

Entropy-based information gain approaches to detect and to characterize gene-gene and gene-environment interactions/correlations of complex diseases

(2011) R. Fan et al.   GENETIC EPIDEMIOLOGY

Modeling of environmental and genetic interactions with AMBROSIA, an information-theoretic model synthesis method

(2011) P Chanda et al.   HEREDITY

Fluorogenic DNA sequencing in PDMS microreactors

(2011) Peter A Sims et al.   NATURE METHODS

Shannon, Rényie and Tsallis entropy analysis of DNA using phase plane

(2011) J.A. Tenreiro Machado et al.   NONLINEAR ANALYSIS-REAL WORLD APPLICATIONS

SNPsyn: detection and exploration of SNP–SNP interactions

(2011) Tomaz Curk et al.   NUCLEIC ACIDS RESEARCH

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Entropy Based Genetic Association Tests and Gene-Gene Interaction Tests

(2011) Mariza de Andrade et al.   Statistical Applications in Genetics and Molecular Biology

Information Metrics in Genetic Epidemiology

(2011) David L Tritchler et al.   Statistical Applications in Genetics and Molecular Biology

Protein-protein interactions: Making sense of networks via graph-theoretic modeling

(2010) Nataša Pržulj   BIOESSAYS

MISS: a non-linear methodology based on mutual information for genetic association studies in both population and sib-pairs analysis

(2010) Helena Brunel et al.   BIOINFORMATICS

Data structures and compression algorithms for high-throughput sequencing technologies

(2010) Kenny Daily et al.   BMC BIOINFORMATICS

TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach

(2010) Pietro Zoppoli et al.   BMC BIOINFORMATICS

An entropy test for single-locus genetic association analysis

(2010) Manuel Ruiz Marin et al.   BMC GENETICS

Comparison of information-theoretic to statistical methods for gene-gene interactions in the presence of genetic heterogeneity

(2010) Lara Sucheston et al.   BMC GENOMICS

A novel gene network inference algorithm using predictive minimum description length approach

(2010) Vijender Chaitankar et al.   BMC Systems Biology

Quantitative Analysis of Cellular Metabolic Dissipative, Self-Organized Structures

(2010) Ildefonso Martínez de la Fuente   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Ecosystem biogeochemistry considered as a distributed metabolic network ordered by maximum entropy production

(2010) J. J. Vallino   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The maximum entropy production principle: two basic questions

(2010) L. M. Martyushev   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Maximum entropy production and plant optimization theories

(2010) R. C. Dewar   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Scaling properties and fractality in the distribution of coding segments in eukaryotic genomes revealed through a block entropy approach

(2010) Labrini Athanasopoulou et al.   PHYSICAL REVIEW E

Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks

(2010) Javier De Las Rivas et al.   PLoS Computational Biology

A brief review of molecular information theory

(2010) Thomas D. Schneider   Nano Communication Networks

Information-theoretic gene-gene and gene-environment interaction analysis of quantitative traits

(2009) Pritam Chanda et al.   BMC GENOMICS

A 2D graphical representation of protein sequence and its numerical characterization

(2009) Jia Wen et al.   CHEMICAL PHYSICS LETTERS

The interaction index, a novel information-theoretic metric for prioritizing interacting genetic variations and environmental factors

(2009) Pritam Chanda et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Metabolic network discovery through reverse engineering of metabolome data

(2009) Tunahan Çakır et al.   Metabolomics

Identification of Coevolving Residues and Coevolution Potentials Emphasizing Structure, Bond Formation and Catalytic Coordination in Protein Evolution

(2009) Daniel Y. Little et al.   PLoS One

Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions

(2009) Gregory E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene-Centric Genomewide Association Study via Entropy

(2008) Y. Cui et al.   GENETICS

AMBIENCE: A Novel Approach and Efficient Algorithm for Identifying Informative Genetic and Environmental Associations With Complex Phenotypes

(2008) P. Chanda et al.   GENETICS

Critical Networks Exhibit Maximal Information Diversity in Structure-Dynamics Relationships

(2008) Matti Nykter et al.   PHYSICAL REVIEW LETTERS

An entropy-based approach for testing genetic epistasis underlying complex diseases

(2007) Guolian Kang et al.   JOURNAL OF THEORETICAL BIOLOGY