A Multi-Label Learning Framework for Predicting Chemical Classes and Biological Activities of Natural Products from Biosynthetic Gene Clusters

Linking Plant Secondary Metabolites and Plant Microbiomes: A Review

(2021) Zhiqiang Pang et al.   Frontiers in Plant Science

Target Prediction Model for Natural Products Using Transfer Learning

(2021) Bo Qiang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

antiSMASH 6.0: improving cluster detection and comparison capabilities

(2021) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Deep learning approaches for natural product discovery from plant endophytic microbiomes

(2021) Shiva Abdollahi Aghdam et al.   Environmental Microbiome

Synthetic biology-inspired strategies and tools for engineering of microbial natural product biosynthetic pathways

(2021) Khorshed Alam et al.   BIOTECHNOLOGY ADVANCES

A Machine Learning Bioinformatics Method to Predict Biological Activity from Biosynthetic Gene Clusters

(2021) Allison S. Walker et al.   Journal of Chemical Information and Modeling

Differential Impact of Plant Secondary Metabolites on the Soil Microbiota

(2021) Vadim Schütz et al.   Frontiers in Microbiology

Prediction of Natural Product Classes Using Machine Learning and 13C NMR Spectroscopic Data

(2020) Saúl H. Martínez-Treviño et al.   Journal of Chemical Information and Modeling

Active and repressed biosynthetic gene clusters have spatially distinct chromosome states

(2020) Hans-Wilhelm Nützmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pinpointing secondary metabolites that shape the composition and function of the plant microbiome

(2020) Richard P Jacoby et al.   JOURNAL OF EXPERIMENTAL BOTANY

Assigning the Origin of Microbial Natural Products by Chemical Space Map and Machine Learning

(2020) Alice Capecchi et al.   Biomolecules

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences

(2020) Michael A. Skinnider et al.   Nature Communications

Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi

(2019) Phuong Nguyen Tran et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A specialized metabolic network selectively modulates Arabidopsis root microbiota

(2019) Ancheng C. Huang et al.   SCIENCE

A deep learning genome-mining strategy for biosynthetic gene cluster prediction

(2019) Geoffrey D Hannigan et al.   NUCLEIC ACIDS RESEARCH

A Multi-Label Learning Framework for Drug Repurposing

(2019) Suyu Mei et al.   Pharmaceutics

A computational framework to explore large-scale biosynthetic diversity

(2019) Jorge C. Navarro-Muñoz et al.   Nature Chemical Biology

Learning representations of microbe–metabolite interactions

(2019) James T. Morton et al.   NATURE METHODS

A Bioinformatics Guide to Plant Microbiome Analysis

(2019) Rares Lucaciu et al.   Frontiers in Plant Science

Current strategies to induce secondary metabolites from microbial biosynthetic cryptic gene clusters

(2018) Jyotsna Begani et al.   ANNALS OF MICROBIOLOGY

Accessing Bioactive Natural Products from the Human Microbiome

(2018) Aleksandr Milshteyn et al.   Cell Host & Microbe

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins

(2018) Auke J van Heel et al.   NUCLEIC ACIDS RESEARCH

Predictive classifier models built from natural products with antimalarial bioactivity using machine learning approach

(2018) Samuel Egieyeh et al.   PLoS One

plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters

(2017) Satria A. Kautsar et al.   NUCLEIC ACIDS RESEARCH

Discovery of MRSA active antibiotics using primary sequence from the human microbiome

(2016) John Chu et al.   Nature Chemical Biology

Synthetic biology to access and expand nature's chemical diversity

(2016) Michael J. Smanski et al.   NATURE REVIEWS MICROBIOLOGY

Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways

(2015) Suyu Mei et al.   BMC BIOINFORMATICS

Computational approaches to natural product discovery

(2015) Marnix H Medema et al.   Nature Chemical Biology

Secondary metabolites in plant innate immunity: conserved function of divergent chemicals

(2015) Anna Piasecka et al.   NEW PHYTOLOGIST

Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters

(2014) Peter Cimermancic et al.   CELL

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

(2013) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives

(2013) K. Schlaeppi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

(2011) Marnix H. Medema et al.   NUCLEIC ACIDS RESEARCH

SMURF: Genomic mapping of fungal secondary metabolite clusters

(2010) Nora Khaldi et al.   FUNGAL GENETICS AND BIOLOGY

Automated genome mining for natural products

(2009) Michael HT Li et al.   BMC BIOINFORMATICS

ClustScan : an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures

(2008) Antonio Starcevic et al.   NUCLEIC ACIDS RESEARCH