Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight

Network Analysis of Gene Transcriptions of Arabidopsis thaliana in Spaceflight Microgravity

(2021) Vidya Manian et al.   Genes

ATM, ATR and DNA-PKcs kinases—the lessons from the mouse models: inhibition ≠ deletion

(2020) Demis Menolfi et al.   Cell and Bioscience

NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models

(2020) J. Tyson McDonald et al.   Cancers

A Guide to Conquer the Biological Network Era Using Graph Theory

(2020) Mikaela Koutrouli et al.   Frontiers in Bioengineering and Biotechnology

Genetic Consequences of Acute/Chronic Gamma and Carbon Ion Irradiation of Arabidopsis thaliana

(2020) Yoshihiro Hase et al.   Frontiers in Plant Science

Developmental, Morphological and Physiological Traits in Plants Exposed for Five Generations to Chronic Low-Level Ionising Radiation

(2020) Nicol M. Caplin et al.   Frontiers in Plant Science

Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling

(2020) Lisa Van den Broeck et al.   Frontiers in Genetics

Variation in the transcriptome of different ecotypes of Arabidopsis thaliana reveals signatures of oxidative stress in plant responses to spaceflight

(2019) Won-Gyu Choi et al.   AMERICAN JOURNAL OF BOTANY

Three-Fast-Inter Incremental Association Markov Blanket learning algorithm

(2019) Xianglin Yang et al.   PATTERN RECOGNITION LETTERS

A regulatory module controlling stress-induced cell cycle arrest in Arabidopsis

(2019) Naoki Takahashi et al.   eLife

On the Origin of Biomolecular Networks

(2019) Heeralal Janwa et al.   Frontiers in Genetics

Spaceflight-induced alternative splicing during seedling development in Arabidopsis thaliana

(2019) Nicole S. Beisel et al.   NPJ Microgravity

Beyond Arabidopsis: Differential UV-B Response Mediated by UVR8 in Diverse Species

(2019) Vanesa Eleonora Tossi et al.   Frontiers in Plant Science

Assessing the Effectiveness of Causality Inference Methods for Gene Regulatory Networks

(2018) Syed Sazzad Ahmed et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

On the role of sparseness in the evolution of modularity in gene regulatory networks

(2018) Carlos Espinosa-Soto   PLoS Computational Biology

Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties

(2018) Wilberforce Zachary Ouma et al.   PLoS Computational Biology

A comparison of methods for inferring causal relationships between genotype and phenotype using additional biological measurements

(2017) Holly F. Ainsworth et al.   GENETIC EPIDEMIOLOGY

Comparison of alternative approaches for analysing multi-level RNA-seq data

(2017) Irina Mohorianu et al.   PLoS One

Genetic dissection of the Arabidopsis spaceflight transcriptome: Are some responses dispensable for the physiological adaptation of plants to spaceflight?

(2017) Anna-Lisa Paul et al.   PLoS One

Quantifying Gene Regulatory Relationships with Association Measures: A Comparative Study

(2017) Zhi-Ping Liu   Frontiers in Genetics

Bridging Plant and Human Radiation Response and DNA Repair through an In Silico Approach

(2017) Zacharenia Nikitaki et al.   Cancers

Transcriptome and proteome responses in RNAlater preserved tissue of Arabidopsis thaliana

(2017) Colin P. S. Kruse et al.   PLoS One

DiffSLC: A graph centrality method to detect essential proteins of a protein-protein interaction network

(2017) Divya Mistry et al.   PLoS One

Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network

(2016) Navadon Khunlertgit et al.   BMC BIOINFORMATICS

Applications of Random Walk Model on Biological Networks

(2016) Wei Peng et al.   Current Bioinformatics

Space Radiation and Human Exposures, A Primer

(2016) Gregory A. Nelson   RADIATION RESEARCH

High atomic weight, high-energy radiation (HZE) induces transcriptional responses shared with conventional stresses in addition to a core “DSB” response specific to clastogenic treatments

(2014) Victor Missirian et al.   Frontiers in Plant Science

Organ-specific remodeling of the Arabidopsis transcriptome in response to spaceflight

(2013) Anna-Lisa Paul et al.   BMC PLANT BIOLOGY

Using networks to measure similarity between genes: association index selection

(2013) Juan I Fuxman Bass et al.   NATURE METHODS

DNA Damage Sensing by the ATM and ATR Kinases

(2013) A. Marechal et al.   Cold Spring Harbor Perspectives in Biology

Spaceflight Transcriptomes: Unique Responses to a Novel Environment

(2012) Anna-Lisa Paul et al.   ASTROBIOLOGY

Learning Bayesian network structure using Markov blanket decomposition

(2012) Anh Tuan Bui et al.   PATTERN RECOGNITION LETTERS

A Markov-Blanket-Based Model for Gene Regulatory Network Inference

(2009) Ramesh Ram et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Light-dependent regulation of carotenoid biosynthesis in plants

(2009) Lorena Pizarro et al.   Ciencia e Investigacion Agraria

LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data

(2008) Maureen A. Sartor et al.   BIOINFORMATICS

Biosynthesis of plant pigments: anthocyanins, betalains and carotenoids

(2008) Yoshikazu Tanaka et al.   PLANT JOURNAL