Michael Warren Lloyd- Ph.D.
- Associate Computational Scientist at The Jackson Laboratory
Michael Warren Lloyd
- Ph.D.
- Associate Computational Scientist at The Jackson Laboratory
About
60
Publications
19,732
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1,510
Citations
Introduction
Current institution
Additional affiliations
June 2009 - June 2009
Workshop on Molecular Evolution: Special Session on Phylogenetics
Position
- Research Assistant
January 2009 - January 2009
Workshop on Molecular Evolution
Position
- Research Assistant
August 2007 - May 2008
Position
- Research Assistant
Description
- Teaching assistant for laboratory sections for PLSC 253/254: Woody Plants for Mid-Atlantic Landscapes I/II
Education
June 2007 - August 2012
August 2005 - May 2007
August 2001 - May 2005
Publications
Publications (60)
Obtaining sequence data from historical museum specimens has been a growing research interest, invigorated by next-generation sequencing methods that allow inputs of highly degraded DNA. We applied a target enrichment and next-generation sequencing protocol to generate ultraconserved elements (UCEs) from 51 large carpenter bee specimens (genus Xylo...
Premise of the study:
Pollen dispersal is a key process that influences ecological and evolutionary dynamics of plant populations by facilitating sexual reproduction and gene flow. Habitat loss and fragmentation have the potential to reduce pollen dispersal within and among habitat patches. We assessed aquatic pollen dispersal and mating system ch...
Patient-Derived Xenografts (PDXs) are tumor-in-mouse models for cancer. PDX collections, such as those supported by the NCI PDXNet program, are powerful resources for preclinical therapeutic testing. However, variations in experimental design and analysis procedures have limited interpretability. To determine the robustness of PDX studies, the PDXN...
Submersed aquatic macrophyte beds provide important ecosystem services, yet their distribution and extent has declined worldwide
in aquatic ecosystems. Effective restoration of these habitats will require, among other factors, reintroduction of genetically
diverse source material that can withstand short- and long-term environmental fluctuations in...
The goal of ecological restoration is to re-establish self-sustaining ecosystems that will resist future perturbation without additional human input. We focus here on the re-establishment of submersed aquatic macrophyte beds in the restoration of the Chesapeake Bay estuary. Degraded environmental conditions are often to blame for poor bed establish...
Short tandem repeat (STR) profiling is commonly performed for authentication of biomedical models of human origin, yet no tools exist to easily compare sets of STR profiles to each other or an existing database in a high-throughput manner. Here, we present STRprofiler, a Python package, command line tool, and Shiny application providing methods for...
Fungus-farming ants cultivate multiple lineages of fungi for food, but, because fungal cultivar relationships are largely unresolved, the history of fungus-ant coevolution remains poorly known. We designed probes targeting >2000 gene regions to generate a dated evolutionary tree for 475 fungi and combined it with a similarly generated tree for 276...
Precision medicine holds great promise for improving cancer outcomes. Yet, there are large inequities in the demographics of patients from whom genomic data and models, including patient-derived xenografts (PDX), are developed and for whom treatments are optimized. In this study, we developed a genetic ancestry pipeline for the Cancer Genomics Clou...
Patient-derived xenografts (PDX) model human intra- and intertumoral heterogeneity in the context of the intact tissue of immunocompromised mice. Histologic imaging via hematoxylin and eosin (H&E) staining is routinely performed on PDX samples, which could be harnessed for computational analysis. Prior studies of large clinical H&E image repositori...
Although patient-derived xenografts (PDXs) are commonly used for preclinical modeling in cancer research, a standard approach to in vivo tumor growth analysis and assessment of antitumor activity is lacking, complicating comparison of different studies and determination of whether a PDX experiment has produced evidence needed to consider a new ther...
The PIVOT program (https://preclinicalpivot.org) is a National Cancer Institute (NCI) funded initiative in support of the RACE Act that funds collaborations between academic centers and industry partners to test the efficacy of targeted cancer treatments developed for adult oncology for potential application in diverse pediatric cancers, including...
Personalized medicine holds great promise for improving cancer outcomes, yet there is a large inequity in the demographics of patients from whom genomic data and models, including patient derived xenografts (PDX), are developed and for whom treatments are optimized. In this study we develop a genetic ancestry pipeline for the Cancer Genomics Cloud,...
Background: BRCA deficient Triple negative breast cancers (TNBC) are effectively treated with platinum agents but, upon relapse, resistance is common. A number of genes have been shown to mediate chemoresistance in vitro, but none have been clinically useful due to the heterogeneous mechanisms of in vivo tumor chemo-resilience. Methods: We attacked...
Personalized medicine holds great promise for improving cancer outcomes, yet there is a large inequity in the demographics of patients from whom genomic data and models, including patient derived xenografts (PDX), are developed and for whom treatments are optimized. In this study we develop a genetic ancestry pipeline for the Cancer Genomics Cloud,...
Patient-derived xenograft (PDX) models are an effective preclinical in vivo platform for testing the efficacy of novel drugs and drug combinations for cancer therapeutics. Here we describe a repository of 79 genomically and clinically annotated lung cancer PDXs available from The Jackson Laboratory that have been extensively characterized for histo...
We created the PDX Network (PDXNet) portal (https://portal.pdxnetwork.org/) to centralize access to the National Cancer Institute-funded PDXNet consortium resources, to facilitate collaboration among researchers and to make these data easily available for research. The portal includes sections for resources, analysis results, metrics for PDXNet act...
Patient-derived xenograft models (PDXs) are an effective preclinical in vivo platform for testing the efficacy of novel drug and drug combinations for cancer therapeutics. Here we describe a repository of 79 genomically and clinically annotated lung cancer PDXs available from The Jackson Laboratory that have been extensively characterized for histo...
Development of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusi...
We created the PDX Network (PDXNet) Portal (https://portal.pdxnetwork.org/) to centralize access to the National Cancer Institute-funded PDXNet consortium resources (i.e., PDX models, sequencing data, treatment response data, and bioinformatics workflows), to facilitate collaboration among researchers, and to make resources easily available for res...
A Correction to this paper has been published: https://doi.org/10.1038/s41588-021-00811-4.
Patient-derived xenografts (PDXs) are resected human tumors engrafted into mice for preclinical studies and therapeutic testing. It has been proposed that the mouse host affects tumor evolution during PDX engraftment and propagation, affecting the accuracy of PDX modeling of human cancer. Here, we exhaustively analyze copy number alterations (CNAs)...
p>Patient-derived xenografts (PDXs) are resected human tumors engrafted into mice for preclinical studies and therapeutic testing. It has been proposed that the mouse host affects tumor evolution during PDX engraftment and propagation, which could impact the capacity of PDXs for faithful modeling of patient treatment response. Such results contrast...
Patient-Derived Xenografts (PDXs) are preclinical models largely used to study tumor biology and drug response. Recent literature highlighted the possibility that growth of human tumors in a mouse microenvironment imposes a selection driving mouse-specific genetic evolution of PDXs, which may compromise their reliability as human cancer models. Con...
The diverse superfamily Oestroidea with more than 15 000 known species includes among others blow flies, flesh flies, bot flies and the diverse tachinid flies. Oestroidea exhibit strikingly divergent morphological and ecological traits, but even with a variety of data sources and inferences there is no consensus on the relationships among major Oes...
The Neotropical realm harbours unparalleled species richness and hence has challenged biologists to explain the cause of its high biotic diversity. Empirical studies to shed light on the processes underlying biological diversification in the Neotropics are focused mainly on vertebrates and plants, with little attention to the hyperdiverse insect fa...
Nylanderia (Emery) is one of the world’s most diverse ant genera, with 123
described species worldwide and hundreds more undescribed. Fifteen globetrotting or
invasive species have widespread distributions and are often encountered outside their
native ranges. A molecular approach to understanding the evolutionary history and to
revision of Nylande...
Patient-derived xenografts (PDXs) are resected human tumors engrafted into mice for preclinical studies and therapeutic testing. It has been proposed that the mouse host affects tumor evolution during PDX engraftment and propagation, impacting the accuracy of PDX modeling of human cancer. Here we exhaustively analyze copy number alterations (CNAs)...
Phylogenomic methods have proven useful for resolving deep nodes and recalcitrant groups in the spider tree of life. Across arachnids, transcriptomic approaches may generate thousands of loci, and target‐capture methods, using the previously designed arachnid‐specific probe‐set, can target a maximum of about 1,000 loci. Here, we develop a specializ...
The evolution of ant agriculture, as practised by the fungus-farming "attine" ants, is thought to have arisen in the wet rainforests of South America about 55-65 Ma. Most subsequent attine agricultural evolution, including the domestication event that produced the ancestor of higher attine cultivars, is likewise hypothesized to have occurred in Sou...
Ants in the Neotropical genus Sericomyrmex Mayr cultivate fungi for food. Both ants and fungi are obligate, coevolved symbionts. The taxonomy of Sericomyrmex is problematic because the morphology of the worker caste is generally homogeneous across all of the species within the genus, species limits are vague, and the relationships between them are...
Context
Submersed aquatic vegetation (SAV) performs water quality enhancing functions that are critical to the overall health of estuaries such as the Chesapeake Bay. However, eutrophication and sedimentation have decimated the Bay’s SAV population to a fraction of its historical coverage. Understanding the spatial distribution of and connectedness...
Additional trees from analyses including outgroups.
(A) Maximum likelihood best tree of 51 Xylocopa specimens, based on 828 UCE loci and 268566 bp (50% matrix), with values from bootstrap analysis mapped onto this tree. (B) Maximum Likelihood best tree of 51 Xylocopa specimens, based on 123 UCE loci and 42753 bp (70% matrix), with values from boots...
Collection data of Xylocopa specimens included in the study.
Summary of collection information for the 51 Xylocopa specimens sequenced in this study, including USNMENT voucher number, collection date, country, locality and coordinates. All information has been transcribed from label data and amended for clarity. Wherever possible, localities have b...
Acropyga ants are a widespread clade of small subterranean formicines that live in obligate symbiotic associations with root mealybugs. We generated a data set of 944 loci of ultraconserved elements (UCEs) to reconstruct the phylogeny of 41 representatives of 23 Acropyga species using both concatenation and species-tree approaches. We investigated...
Background
Ultraconserved elements (UCEs) have been successfully used in phylogenomics for a variety of taxa, but their power in phylogenetic inference has yet to be extensively compared with that of traditional Sanger sequencing data sets. Moreover, UCE data on invertebrates, including insects, are sparse. We compared the phylogenetic informativen...
All available evidence suggests that genetic diversity is important for ecological performance and resil-
ience through the expression and variance of phenotypic traits. Genetic diversity is a multiscalar variable;
it includes heterozygosity at the individual scale, genotypic diversity at the population scale, and local
adaptation at the regional s...
Habitat loss and fragmentation are imminent threats to biological diversity worldwide and thus are fundamental issues in conservation biology. Increased isolation alone has been implicated as a driver of negative impacts in populations associated with fragmented landscapes. Genetic monitoring and the use of measures of genetic divergence have been...
Use of genetic methods to estimate effective population size (Ne) is rapidly increasing, but all approaches make simplifying assumptions unlikely to be met in real populations. In particular, all assume a single, unstructured population, and none has been evaluated for use with continuously distributed species. We simulated continuous populations w...
The objective my dissertation was to assess the effects of habitat loss and fragmentation on genetic diversity and landscape connectivity. I focused on Vallisneria americana Michx. (Hydrocharitaceae), a submersed aquatic plant species found in the Chesapeake Bay. Vallisneria americana has undergone dramatic changes in abundance and distribution thr...
Arabidopsis lyrata ssp. lyrata is widespread but edaphically restricted, which suggests that the dispersal ability and level of genetic exchange among populations might be limited. We assessed levels of genetic diversity and population differentiation within and among six A. lyrata ssp. lyrata populations from along the eastern seaboard of the Unit...
Vallisneria americana Michaux (wild celery) is currently a target of submersed aquatic vegetation restoration efforts in the Chesapeake Bay watershed. To aid these efforts, we have developed 11 polymorphic microsatellite markers to assess the distribution and degree of genetic diversity in both restored and naturally occurring populations in the Ch...
Questions
Questions (2)
I've been watching Silicon Valley on HBO, which focuses on a fictitious compression algorithm company. It got me thinking, files that come off a HiSeq/MiSeq run can be huge, but they are basically glorified text files. Is anyone out there working on better compression of these types of files? The amount of data being generated is fast outstripping storage capacity. Illumina is also now charging for cloud storage of these files once you have over a TB of data. Obviously, if you can store more with less...all the better. So, is there anyone out there doing this type of work, or know of a method of compression that shrinks this type of file beyond what the basic gzip/tarball can do?
I did a genomic DNA extraction of fungal tissue using a CTAB/phenol based automated extraction. To my knowledge the samples were not treated with prot K or RNAase during the process.
When I look at the genomic DNA on a gel, I see unexplained smeared bands below 50bp, with additional smearing below that. I ran the attached gel in attached image too long, and the smear bled into the wells below. The 1.5% gel was stained with GelRed, and run at 100v for 40min.
Does anyone know what this low molecular weight band and smearing could be?
