Data integration and predictive modeling methods for multi-omics datasets
M Kim, I Tagkopoulos - Molecular omics, 2018 - pubs.rsc.org
Translating data to knowledge and actionable insights is the Holy Grail for many scientific
fields, including biology. The unprecedented massive and heterogeneous data have created …
fields, including biology. The unprecedented massive and heterogeneous data have created …
iML1515, a knowledgebase that computes Escherichia coli traits
Figure 1 iML1515 genome-scale reconstruction.(a) The iML1515 model contains 1,515
open reading frames that encode enzymes that catalyze 2,719 reactions involving 1,192 …
open reading frames that encode enzymes that catalyze 2,719 reactions involving 1,192 …
An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network
ML Arrieta‐Ortiz, C Hafemeister, AR Bate… - Molecular systems …, 2015 - embopress.org
Organisms from all domains of life use gene regulation networks to control cell growth,
identity, function, and responses to environmental challenges. Although accurate global …
identity, function, and responses to environmental challenges. Although accurate global …
A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives
J Hafner, J Payne, H MohammadiPeyhani… - Nature …, 2021 - nature.com
Plant natural products (PNPs) and their derivatives are important but underexplored sources
of pharmaceutical molecules. To access this untapped potential, the reconstitution of …
of pharmaceutical molecules. To access this untapped potential, the reconstitution of …
Independent component analysis recovers consistent regulatory signals from disparate datasets
The availability of bacterial transcriptomes has dramatically increased in recent years. This
data deluge could result in detailed inference of underlying regulatory networks, but the …
data deluge could result in detailed inference of underlying regulatory networks, but the …
Methods used in microbial forensics and epidemiological investigations for stronger health systems
AE Castro, MCA De Ungria - Forensic Sciences Research, 2022 - academic.oup.com
This review discusses microbial forensics as an emerging science that finds application in
protecting human health. It is important to distinguish naturally acquired infections from …
protecting human health. It is important to distinguish naturally acquired infections from …
Hiding in plain sight: mining bacterial species records for phenotypic trait information
Cultivation in the laboratory is essential for understanding the phenotypic characteristics and
environmental preferences of bacteria. However, basic phenotypic information is not readily …
environmental preferences of bacteria. However, basic phenotypic information is not readily …
Compendium-wide analysis of Pseudomonas aeruginosa core and accessory genes reveals transcriptional patterns across strains PAO1 and PA14
Pseudomonas aeruginosa is an opportunistic pathogen that causes difficult-to-treat
infections. Two well-studied divergent P. aeruginosa strain types, PAO1 and PA14, have …
infections. Two well-studied divergent P. aeruginosa strain types, PAO1 and PA14, have …
Predicting the evolution of Escherichia coli by a data-driven approach
A tantalizing question in evolutionary biology is whether evolution can be predicted from
past experiences. To address this question, we created a coherent compendium of more …
past experiences. To address this question, we created a coherent compendium of more …
Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota
Studies involving gut microbiome analysis play an increasing role in the evaluation of health
and disease in humans and animals alike. Fecal sampling methods for DNA preservation in …
and disease in humans and animals alike. Fecal sampling methods for DNA preservation in …