Zamin Iqbal
Computational biologist: Pathogens, genomics, genome graphs, antibiotic resistance, direct-from-sputum TB diagnostics, global surveillance of bacteria
Thought Leader
| #154 | Infectious Disease |
Last synced from Twitter 81d ago
Exploration of Bacterial Bottlenecks and Streptococcus pneumoniae Pathogenesis by CRISPRi-Seq
Liu et al. developed CRISPRi-seq to enable in vivo genome-wide fitness testing of
Streptococcus pneumoniae in one sequencing step. CRISPRi-seq revealed a bottleneck
during murine pneumococcal infection not observed upon influenza virus...
The PfAP2-G2 transcription factor is a critical regulator of gametocyte maturation
Differentiation from asexual blood stages to sexual gametocytes is required for transmission of malaria parasites from the human to the mosquito host. Preventing gametocyte commitment and development would block parasite transmission, but the...
Systematic investigation of resistance evolution to common antibiotics reveals conserved collateral responses across common human pathogens.
As drug resistance continues to grow, treatment strategies that turn resistance into a disadvantage for the organism will increasingly be relied upon to treat infections and to slow the rate of multidrug resistance. The majority of work in this area...
Three-dimensional biofilm growth supports a mutualism involving matrix and nutrient sharing
Life in a three-dimensional structure such as a biofilm is typical for many bacteria, yet little is known about how strains with different genotypes interact in this context. Here, to systematically explore gene knockdowns across various...
Drivers and sites of diversity in the DNA adenine methylomes of 93 Mycobacterium tuberculosis complex clinical isolates
Fully assembled DNA methylomes from phylogeographically diverse clinical Mycobacterium tuberculosis complex isolates reveals 'intercellular mosaic methylation' as a source of epigenetic diversity.
Vince Guaraldi Trio - Linus And Lucy
Music video by Vince Guaraldi Trio performing Linus And Lucy. (C) 2012 Concord Music Group, Inc.
Zamin Iqbal
For those of a certain age
82d
A curated dataset of modern and ancient high-coverage shotgun human genomes.
Over the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of capture SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain type of analyses...
A2B-COVID: A method for evaluating potential SARS-CoV-2 transmission events
Identifying linked cases of infection is a key part of the public health response to viral infectious disease. Viral genome sequence data is of great value in this task, but requires careful analysis, and may need to be complemented by additional...
The Central Role of Interbacterial Antagonism in Bacterial Life
Peterson et al. argue that interbacterial interactions, in particular antagonistic
interactions, have played an important, underappreciated role in the evolution of
bacteria and the structuring of bacterial communities.
Release Version 0.2.3 · snakemake/snakefmt
Added
Add a vim plugin to snakefmt [#62] and instructions to use it
New searching for project configuration. Used to look for pyproject.toml in current working directory, now recursively search fo...
Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control
In humans and nonhuman primates, Mycobacterium tuberculosis lung infection yields a complex multicellular structure: the tuberculosis granuloma. All granulomas are not equivalent, however, even within the same host: in some, local immune activity...
Identification of the conjugative and mobilizable plasmid fragments in the plasmidome using sequence signatures | Microbiology Society
Plasmids are the key element in horizontal gene transfer in the microbial community. Recently, a large number of experimental and computational methods have been developed to obtain the plasmidomes of microbial communities. Distinguishing...
Trade-Offs Between Antibacterial Resistance and Fitness Cost in the Production of Metallo-β-Lactamase by Enteric Bacteria Manifest as Sporadic Emergence of Carbapenem Resistance in a Clinical Setting.
Meropenem is a clinically important antibacterial reserved for treatment of multi-resistant infections. In meropenem-resistant bacteria of the family Enterobacteriales, NDM-1 is considerably more common than IMP-1, despite both metallo-β-lactamases...
The seventh pandemic of cholera in Europe revisited by microbial genomics
Since 1970, several cholera outbreaks caused by the “seventh pandemic” (7PET) lineage have been reported in Europe. Here, the authors demonstrate that the outbreaks were caused by repeated introductions of 7PET into Europe, rather than local...
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A role for fibroblast growth factor receptor 1 in the pathogenesis of Neisseria meningitidis
Neisseria meningitidis (the meningococcus) remains an important cause of human disease, including meningitis and sepsis. Adaptation to the host enviro…