Nature Search

A progesterone biosensor derived from microbial screening

Bacteria represent an unexploited reservoir of biosensing proteins. Here the authors use genomic screens and functional assays to isolate a progesterone sensing allosteric transcription factor and use a FRET-based method to develop an optical progesterone sensor.

Chloé Grazon
R C. Baer
James E. Galagan
ResearchOpen Access09 Mar 2020
Nature Communications

Volume: 11, P: 1-10
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

James E. Galagan
Sarah E. Calvo
Bruce W. Birren
Research22 Dec 2005
Nature

Volume: 438, P: 1105-1115
Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli

The authors describe BoltzNet, a neural network that learns the energy of transcription factor (TF)-DNA binding from genomic data and can be used to design new binding sites. They report the in vivo mapping and BoltzNet modeling of 139 E. coli TFs.

Patrick Lally
Laura Gómez-Romero
James E. Galagan
ResearchOpen Access07 May 2025
Nature Communications

Volume: 16, P: 1-16
Genome sequencing and analysis of Aspergillus oryzae

Masayuki Machida
Kiyoshi Asai
Hisashi Kikuchi
Research22 Dec 2005
Nature

Volume: 438, P: 1157-1161
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

William C. Nierman
Arnab Pain
David W. Denning
Research22 Dec 2005
Nature

Volume: 438, P: 1151-1156
Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance

Ashlee Earl and colleagues analyze whole-genome sequences from 5,310 Mycobacterium tuberculosis isolates from five continents. They find that resistance to isoniazid arises before rifampicin resistance across all of the lineages, geographical regions and time periods.

Abigail L Manson
Keira A Cohen
Ashlee M Earl
Research16 Jan 2017
Nature Genetics

Volume: 49, P: 395-402
The DNA-binding network of Mycobacterium tuberculosi s

Adaptation of Mycobacterium tuberculosis to the host environment is principally mediated through its transcription factors. Here, the authors report the DNA binding and transcriptional profile of ~80% of all predicted M. tuberculosistranscription factors, and find wide-spread dormant DNA binding.

Kyle J. Minch
Tige R. Rustad
David R. Sherman
ResearchOpen Access12 Jan 2015
Nature Communications

Volume: 6, P: 1-10
Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

Maha Farhat, Megan Murray and colleagues report whole-genome sequencing of 116 Mycobacterium tuberculosis strains selected to be representative of both global diversity and drug resistance. The authors develop a new method to search for resistance markers in microbial genomes based on reconstructing a genome-wide phylogeny and identifying regions showing convergent evolution, and they use this method to identify 39 new candidate drug resistance regions in the M. tuberculosis genome.

Maha R Farhat
B Jesse Shapiro
Megan Murray
Research01 Sept 2013
Nature Genetics

Volume: 45, P: 1183-1189
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

Fungi from the genus Fusarium are important pathogens of animals and crop plants. Some have a wide host range, whereas others are more specific in the organisms they infect. Here, clues are provided as to how differences in specificity come about. The genomes of two Fusarium fungi with differing host ranges have been sequenced, and compared with the genome of a third species. Experiments show that transferring two whole chromosomes turns a non-pathogenic Fusarium strain into a pathogenic one.

Li-Jun Ma
H. Charlotte van der Does
Martijn Rep
ResearchOpen Access18 Mar 2010
Nature

Volume: 464, P: 367-373
The genome sequence of the rice blast fungus Magnaporthe grisea

Ralph A. Dean
Nicholas J. Talbot
Bruce W. Birren
ResearchOpen Access21 Apr 2005
Nature

Volume: 434, P: 980-986
The Mycobacterium tuberculosis regulatory network and hypoxia

Mycobacterium tuberculosis has the ability to survive within the host for months to decades in an asymptomatic state, and adaptations to hypoxia are thought to have an important role in pathogenesis; here a systems-wide reconstruction of the regulatory network provides a framework for understanding mycobacterial persistence in the host.

James E. Galagan
Kyle Minch
Gary K. Schoolnik
Research03 Jul 2013
Nature

Volume: 499, P: 178-183
The genome sequence of the filamentous fungus Neurospora crassa

James E. Galagan
Sarah E. Calvo
Bruce Birren
ResearchOpen Access24 Apr 2003
Nature

Volume: 422, P: 859-868
Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

Sebastien Gagneux and colleagues report the genome sequences of 21 phylogeographically diverse Mycobacterium tuberculosis complex strains. Analysis of the global genetic diversity of these strains showed that most of the known human T cell epitopes were highly conserved.

Iñaki Comas
Jaidip Chakravartti
Sebastien Gagneux
Research23 May 2010
Nature Genetics

Volume: 42, P: 498-503
Genomic insights into tuberculosis

This Review describes how genomic technologies are providing novel insights intoMycobacterium tuberculosis, which is the causative agent of human tuberculosis. There has been progress in understanding the ancient evolutionary history of human-adapted M. tuberculosis, mutations underlying strain diversity and drug resistance, and the host–pathogen molecular interactions.

James E. Galagan
Reviews25 Mar 2014
Nature Reviews Genetics

Volume: 15, P: 307-320
Correction: Corrigendum: Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

William C. Nierman
Arnab Pain
David W. Denning
Amendments and Corrections26 Jan 2006
Nature

Volume: 439, P: 502
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

Jörg Kämper
Regine Kahmann
Bruce W. Birren
ResearchOpen Access02 Nov 2006
Nature

Volume: 444, P: 97-101
Green fabrication of stable lead-free bismuth based perovskite solar cells using a non-toxic solvent

Perovskites are widely studied as components of solar cells but their synthesis often involves toxic reagents. Here lead-free bismuth-based perovskites are synthesised using a non-toxic solvent and shown to achieve power conversion efficiencies of up to 1.62 % under 1 sun illumination for up to 300 h.

Sagar M. Jain
Tomas Edvinsson
James R. Durrant
ResearchOpen Access08 Aug 2019
Communications Chemistry

Volume: 2, P: 1-7
Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

Sarah Fortune and colleagues report the whole-genome sequencing of Mycobacterium tuberculosis strains isolated from cynomolgus macaques with either active, latent or early reactivation disease. They estimate a similar mutation rate for these disease states in vivo, as well as for the bacterium in vitro. This suggests that M. tuberculosis has a greater mutational rate during latent and early reactivation disease than previously predicted and may be able to acquire drug resistance during these states.

Christopher B Ford
Philana Ling Lin
Sarah M Fortune
Research24 Apr 2011
Nature Genetics

Volume: 43, P: 482-486
Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes

Sebastien Gagneux and colleagues identify a set of compensatory mutations in the RNA polymerase of rifampicin-resistant M. tuberculosis by comparing the whole-genome sequences of ten paired clinical isolates and strains evolved in vitro. These mutations are associated with high competitive fitness in vitro and occur with increased clinical frequency in affected populations with a high burden of drug-resistant tuberculosis.

Iñaki Comas
Sonia Borrell
Sebastien Gagneux
Research18 Dec 2011
Nature Genetics

Volume: 44, P: 106-110
A genome-wide map of diversity in Plasmodium falciparum

Sarah K Volkman
Pardis C Sabeti
Dyann F Wirth
Research10 Dec 2006
Nature Genetics

Volume: 39, P: 113-119
Redefining fundamental concepts of transcription initiation in bacteria

In this Expert Recommendation, the authors review the definitions of classic concepts relating to bacterial gene regulation, with a focus on transcription initiation, and suggest up-to-date, precise definitions to provide a reference for knowledge representation, modelling and future research on bacterial gene regulation.

Citlalli Mejía-Almonte
Stephen J. W. Busby
Julio Collado-Vides
Reviews14 Jul 2020
Nature Reviews Genetics

Volume: 21, P: 699-714
Initial sequencing and analysis of the human genome

Eric S. Lander
Lauren M. Linton
Michael J. Morgan
articles01 Feb 2001
Nature

Volume: 409, P: 860-921

Search

A progesterone biosensor derived from microbial screening

Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli

Genome sequencing and analysis of Aspergillus oryzae

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance

The DNA-binding network of Mycobacterium tuberculosi s

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

The genome sequence of the rice blast fungus Magnaporthe grisea

The Mycobacterium tuberculosis regulatory network and hypoxia

The genome sequence of the filamentous fungus Neurospora crassa

Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

Genomic insights into tuberculosis

Correction: Corrigendum: Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

Green fabrication of stable lead-free bismuth based perovskite solar cells using a non-toxic solvent

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes

A genome-wide map of diversity in Plasmodium falciparum

Redefining fundamental concepts of transcription initiation in bacteria

Initial sequencing and analysis of the human genome

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