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Article
Open AccessComparison of the transcriptome, lipidome, and c-di-GMP production between BCGΔBCG1419c and BCG, with Mincle- and Myd88-dependent induction of proinflammatory cytokines in murine macrophages
We have previously reported the transcriptomic and lipidomic profile of the first-generation, hygromycin-resistant (HygR) version of the BCGΔBCG1419c vaccine candidate, under biofilm conditions. We recently const...
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Article
Open AccessConsequential insights for advancing informal STEM learning and outcomes for students from historically marginalized communities
Consequential STEM experiences in informal settings can address issues of equity by fully engaging historically marginalized high school students in complex socio-scientific issues. However, inclusive and effe...
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Article
Open AccessA comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS
Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed i...
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Article
Open AccessGrowth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes
Longitudinal sampling of the stool has yielded important insights into the ecological dynamics of the human gut microbiome. However, human stool samples are available approximately once per day, while commensa...
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Article
Open AccessA single-cell based precision medicine approach using glioblastoma patient-specific models
Glioblastoma (GBM) is a heterogeneous tumor made up of cell states that evolve over time. Here, we modeled tumor evolutionary trajectories during standard-of-care treatment using multi-omic single-cell analysi...
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Article
Open AccessQuantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME
The ability of Mycobacterium tuberculosis (Mtb) to adopt heterogeneous physiological states underlies its success in evading the immune system and tolerating antibiotic killing. Drug tolerant phenotypes are a maj...
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Article
Open AccessGenetic program activity delineates risk, relapse, and therapy responsiveness in multiple myeloma
Despite recent advancements in the treatment of multiple myeloma (MM), nearly all patients ultimately relapse and many become refractory to multiple lines of therapies. Therefore, we not only need the ability ...
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Article
Open AccessA comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS
Data-Independent Acquisition (DIA) is a method to improve consistent identification and precise quantitation of peptides and proteins by mass spectrometry (MS). The targeted data analysis strategy in DIA relie...
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Article
EcoFABs: advancing microbiome science through standardized fabricated ecosystems
Microbiomes play critical roles in ecosystems and human health, yet in most cases scientists lack standardized and reproducible model microbial communities. The development of fabricated microbial ecosystems, ...
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Article
Open AccessOcean acidification conditions increase resilience of marine diatoms
The fate of diatoms in future acidified oceans could have dramatic implications on marine ecosystems, because they account for ~40% of marine primary production. Here, we quantify resilience of Thalassiosira pseu...
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Article
Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis
The resilience of Mycobacterium tuberculosis (MTB) emerges from its ability to effectively counteract immunological, environmental and antitubercular challenges. Here, we demonstrate that MTB can tolerate drug tr...
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Article
Open AccessTranscriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii
Algae accumulate lipids to endure different kinds of environmental stresses including macronutrient starvation. Although this response has been extensively studied, an in depth understanding of the transcripti...
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Article
Diatom acclimation to elevated CO2 via cAMP signalling and coordinated gene expression
Carbon fixation by marine diatoms, which dominate ocean primary productivity, is energetically expensive. Now genetic analysis shows that elevated CO2 causes downregulation of these mechanisms, resulting in metab...
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Article
Open AccessBicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions
Biclustering is a popular method for identifying under which experimental conditions biological signatures are co-expressed. However, the general biclustering problem is NP-hard, offering room to focus algorit...
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Article
Open AccessA comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis
Mycobacterium tuberculosis (MTB) is a pathogenic bacterium responsible for 12 million active cases of tuberculosis (TB) worldwide. The complexity and critical regulatory components of MTB pathogenicity are still ...
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Article
Open AccessThe DNA-binding network of Mycobacterium tuberculosi s
Mycobacterium tuberculosis (MTB) infects 30% of all humans and kills someone every 20–30 s. Here we report genome-wide binding for ~80% of all predicted MTB transcription factors (TFs), and assayed global express...
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Article
Open AccessCommunity-integrated omics links dominance of a microbial generalist to fine-tuned resource usage
Microbial communities are complex and dynamic systems that are primarily structured according to their members’ ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strat...
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Article
Open AccessEvolution of context dependent regulation by expansion of feast/famine regulatory proteins
Expansion of transcription factors is believed to have played a crucial role in evolution of all organisms by enabling them to deal with dynamic environments and colonize new environments. We investigated how ...
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Article
Open AccessMap** and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network
Mycobacterium tuberculosis senses and responds to the shifting and hostile landscape of the host. To characterize the underlying intertwined gene regulatory network governed by approximately 200 transcription fac...
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Article
Correction: Corrigendum: Peroxiredoxins are conserved markers of circadian rhythms
Nature 485, 459–464 (2012); doi:10.1038/nature11088 In the author list of this Article, the names of Gerben van Ooijen and Maria Olmedo should also have been asterisked, indicating their equal contributions. T...
