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Finding phenazine

Libusha Kelly, Sarah J Wolfson
2020 eLife  
Copyright Wolfson and Kelly.  ... 
doi:10.7554/elife.62983 pmid:33108273 fatcat:4ywhcrdojfhpzd7l4i7z2ax2mi

Inferring the quasipotential landscape of microbial ecosystems with topological data analysis [article]

William K. Chang, Libusha Kelly
2019 bioRxiv   pre-print
AbstractThe dynamics of high-dimensional, nonlinear systems drive biology at all scales, from gene regulatory networks to ecosystems. Microbial ecosystems ('microbiomes') exemplify such systems due to their richness and the small length- and time-scales of complex ecological and evolutionary dynamics. Microbes inhabit, respond to, and alter environments ranging from the human gut to the ocean. Here, using information theory and topological data analysis [1] (TDA), we model microbiome dynamics
more » ... motion on a potential energy-like landscape, called the quasipotential, identifying attractor states and trajectories that characterize ecological processes including disease progression in the human microbiome and geochemical cycling in the oceans. Our approach allows holistic analysis and prediction of large-scale dynamics in generalized complex systems that are difficult to reduce to their underlying interactions.
doi:10.1101/584201 fatcat:wkw3gytu5fburnq7tql25i3cku

Bringing microbiome-drug interaction research into the clinic

Leah Guthrie, Libusha Kelly
2019 EBioMedicine  
Acknowledgements This work was supported in part by a Peer Reviewed Cancer Research Program Career Development Award from the United States Department of Defense to Libusha Kelly (CA171019); Leah Guthrie  ...  Kelly has nothing to disclose. 1 . 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 709 2.  ... 
doi:10.1016/j.ebiom.2019.05.009 pmid:31151933 pmcid:PMC6604038 fatcat:ycbjusyogng5hir53wszntkfmq

The human gut chemical landscape predicts microbe-mediated biotransformation of foods and drugs

Leah Guthrie, Sarah Wolfson, Libusha Kelly
2019 eLife  
The authors thank the reviewers, members of the Kelly lab and Tyler Grove (Einstein) for helpful suggestions on the work.  ...  Kelly https://orcid.org/0000-0002-7303-1022 Additional files  ...  Kelly, Conceptualization, Supervision, Funding acquisition, Writing-original draft, Writing-review and editing Decision letter and Author response Decision letter https://doi.org/10.7554/eLife.42866.021  ... 
doi:10.7554/elife.42866 pmid:31184303 pmcid:PMC6559788 fatcat:mxcrd2g7gzgatmb6beacwt4xty

PROTEIN INTERACTIONS AND DISEASE PHENOTYPES IN THE ABC TRANSPORTER SUPERFAMILY

LIBUSHA KELLY, RACHEL KARCHIN, ANDREJ SALI
2006 Biocomputing 2007  
. * Corresponding author libusha@salilab.org Pacific Symposium on Biocomputing 12:51-63 (2007) proper function.  ... 
doi:10.1142/9789812772435_0006 fatcat:my5ag4vlxnfvzeti6y4526bwsi

Multiclass Disease Classification from Microbial Whole-Community Metagenomes using Graph Convolutional Neural Networks [article]

Saad Khan, Libusha Kelly
2019 bioRxiv   pre-print
Libusha Kelly is supported in part by a Peer Reviewed Cancer Research Program Career Development Award from the United States Department of Defense (CA171019).  ... 
doi:10.1101/726901 fatcat:esslikyydve4hinucjipchzng4

Fireworks: Reproducible Machine Learning and Preprocessing with PyTorch

Saad Khan, Libusha Kelly
2019 Journal of Open Source Software  
Here, we present a batch-processing library for constructing machine learning pipelines using PyTorch and dataframes. It is meant to provide an easy method to stream data from a dataset into a machine learning model while performing reprocessing steps such as randomization, train/test split, batch normalization, etc. along the way. Fireworks offers more flexibility and structure for constructing input pipelines than the built-in dataset modules in PyTorch (Paszke et al., 2017) , but is also
more » ... t to be easier to use than frameworks such as Apache Spark (Zaharia et al., 2016) .
doi:10.21105/joss.01478 fatcat:ecur6mydlbgsndl27ytfzqywhy

Multiclass Disease Classification from Microbial Whole-Community Metagenomes

Saad Khan, Libusha Kelly
2020 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
Libusha Kelly is supported in part by a Peer Reviewed Cancer Research Program Career Development Award from the United States Department of Defense (CA171019). Fig. 1 . 1 Fig. 1.  ... 
pmid:31797586 pmcid:PMC7120658 fatcat:nvmoyhcn7vgxfbdb25pwohuyva

Resolving the structure of phage-bacteria interactions in the context of natural diversity [article]

Kathryn M Kauffman, William K Chang, Julia M Brown, Fatima Aysha Hussain, Joy Y Yang, Martin F Polz, Libusha Kelly
2021 bioRxiv   pre-print
Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in "the wild" remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain quantitative estimates of strain-level phage predator loads, and use
more » ... -all host range assays to discover how phage and host genomic diversity shape interactions. We show that killing in environmental interaction networks is sparse - with phage predator loads low for most bacterial strains and phages host-strain-specific in their killing. Paradoxically, we also find that although overlap in killing is generally rare between phages, recombination is common. Together, these results indicate that the number of hosts that phages infect is often larger than the number that they kill and suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it will be important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on killing host range.
doi:10.1101/2021.06.27.449121 fatcat:s6izkbawwzguphehqxvfmpq2uy

Human microbiome signatures of differential colorectal cancer drug metabolism

Leah Guthrie, Sanchit Gupta, Johanna Daily, Libusha Kelly
2017 npj Biofilms and Microbiomes  
This work was supported by a grant from the National Science Foundation OCE 1435993 to Libusha Kelly.  ... 
doi:10.1038/s41522-017-0034-1 pmid:29104759 pmcid:PMC5665930 fatcat:xsmhxnlwenguhcy3bqyhv3367q

Comparison of human solute carriers

Avner Schlessinger, Pär Matsson, James E. Shima, Ursula Pieper, Sook Wah Yee, Libusha Kelly, Leonard Apeltsin, Robert M. Stroud, Thomas E. Ferrin, Kathleen M. Giacomini, Andrej Sali
2010 Protein Science  
Scores and significance values were calculated similarly to the procedure described by Pearson 101 and as already applied to membrane proteins (Kelly et al., submitted for publication).  ...  consortia, which aim for complete coverage of integral membrane proteome, 77 because hub structures can serve as templates for computational modeling of many other proteins with similar sequences (Kelly  ... 
doi:10.1002/pro.320 pmid:20052679 pmcid:PMC2866268 fatcat:dk7r2xd2qncezg2jjjzxhzfgiu

Viruses of the Nahant Collection, characterization of 251 marine Vibrionaceae viruses

Kathryn M. Kauffman, Julia M. Brown, Radhey S. Sharma, David VanInsberghe, Joseph Elsherbini, Martin Polz, Libusha Kelly
2018 Scientific Data  
Viruses are highly discriminating in their interactions with host cells and are thought to play a major role in maintaining diversity of environmental microbes. However, large-scale ecological and genomic studies of co-occurring virus-host pairs, required to characterize the mechanistic and genomic foundations of virushost interactions, are lacking. Here, we present the largest dataset of cultivated and sequenced cooccurring virus-host pairs that captures ecologically representative fine-scale
more » ... iversity. Using the ubiquitous and ecologically diverse marine Vibrionaceae as a host platform, we isolate and sequence 251 dsDNA viruses and their hosts from three time points within a 93-day time-series study. The virus collection includes representatives of the three Caudovirales tailed virus morphotypes, a novel family of nontailed viruses, and the smallest (10,046 bp) and largest (348,911 bp) Vibrio virus genomes described. We provide general characterization and annotation of the viruses and describe read-mapping protocols to standardize genome presentation. The rich ecological and genomic contextualization of hosts and viruses make the Nahant Collection a unique platform for high-resolution studies of environmental virus-host infection networks. Design Type(s) time series design • biodiversity assessment objective Measurement Type(s) genome assembly Technology Type(s) DNA sequencing Factor Type(s) temporal_instant Sample Characteristic(s) dsDNA viruses, no RNA stage • Nahant • coastal sea water
doi:10.1038/sdata.2018.114 pmid:29969110 pmcid:PMC6029569 fatcat:loszifeivfhfxaqned56fr45ui

Microbiology and Ecology Are Vitally Important to Premedical Curricula

Val H. Smith, Rebecca J. Rubinstein, Serry Park, Libusha Kelly, Vanja Klepac-Ceraj
2015 Evolution, Medicine and Public Health  
A B S T R A C T Despite the impact of the human microbiome on health, an appreciation of microbial ecology is yet to be translated into mainstream medical training and practice. The human microbiota plays a role in the development of the immune system, in the development and function of the brain, in digestion, and in host defense, and we anticipate that many more functions are yet to be discovered. We argue here that without formal exposure to microbiology and ecology-fields that explore the
more » ... tworks, interactions and dynamics between members of populations of microbes-vitally important links between the human microbiome and health will be overlooked. This educational shortfall has significant downstream effects on patient care and biomedical research, and we provide examples from current research highlighting the influence of the microbiome on human health. We conclude that formally incorporating microbiology and ecology into the premedical curricula is invaluable to the training of future health professionals and critical to the development of novel therapeutics and treatment practices. K E Y W O R D S : premedical curricula; microbiology; human microbiome; ecology ß The Author(s)
doi:10.1093/emph/eov014 pmid:26198190 pmcid:PMC4536855 fatcat:mt37nw6vi5dzxbnuqxkrdd6uam

Topological analysis reveals state transitions in human gut and marine bacterial communities

William K. Chang, David VanInsberghe, Libusha Kelly
2020 npj Biofilms and Microbiomes  
Microbiome dynamics influence the health and functioning of human physiology and the environment and are driven in part by interactions between large numbers of microbial taxa, making large-scale prediction and modeling a challenge. Here, using topological data analysis, we identify states and dynamical features relevant to macroscopic processes. We show that gut disease processes and marine geochemical events are associated with transitions between community states, defined as topological
more » ... res of the data density. We find a reproducible two-state succession during recovery from cholera in the gut microbiomes of multiple patients, evidence of dynamic stability in the gut microbiome of a healthy human after experiencing diarrhea during travel, and periodic state transitions in a marine Prochlorococcus community driven by water column cycling. Our approach bridges small-scale fluctuations in microbiome composition and large-scale changes in phenotype without details of underlying mechanisms, and provides an assessment of microbiome stability and its relation to human and environmental health.
doi:10.1038/s41522-020-00145-9 pmid:33057043 fatcat:xalaoscyqrdgvb63fv65hga54e

Response to "Predictable difficulty or difficulty to predict"

Libusha Kelly, Hisayo Fukushima, Rachel Karchin, Jason M. Gow, Leslie W. Chinn, Ursula Pieper, Mark R. Segal, Deanna L. Kroetz, Andrej Sali
2010 Protein Science  
doi:10.1002/pro.555 pmcid:PMC3047056 fatcat:fkmtmw72krfhjat5ohnc6dg5ky
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