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Postdoctoral Fellow, Computational Biology and Genomics of Mobile Elements
Dr. Yi Xing’s lab at the Children’s Hospital of Philadelphia (CHOP) and the University of Pennsylvania (Penn) is recruiting a postdoctoral fellow to study the roles of mobile elements
in regulating RNA and protein expression in human cells. Our lab is broadly interested in computational biology and genomics of RNA processing and regulation, as well as their applications to human genetics, precision medicine, and cancer immunotherapy. We develop computational methods and genomic technologies for studying transcriptomic and proteomic complexity in bulk tissues and single cells
We also integrate computational and genomic tools to elucidate RNA regulatory networks in health and disease . We have a longstanding interest in understanding how mobile elements impact species-specific RNA regulatory networks
and consequently the recent evolution of the human transcriptome and proteome.
We are looking for enthusiastic candidates with outstanding research experience and publication record.
The successful candidates will work in an integrated computational and experimental research
environment, and will have the opportunity to generate and/or analyze large amount of second- and third generation
sequencing data to elucidate how mobile elements shape transcriptome and proteome complexity in healthy or diseased states. We welcome applicants from either computational or experimental background, or a combination of both.
Interested candidates should send a CV and names of three referees to Dr. Yi Xing, at
Yi.Xing@pennmedicine.upenn.edu. For more details of the lab, please visit https://xinglab.org/.
(Posted March 18, 2019)
Postdoctoral Position at University of Lyon
We are seeking a postdoctoral researcher to be hired at the University of Lyon (Biometry and Evolutionary Biology Lab) for three years, starting in September 2019.
The project will deal with horizontal gene transfer in insects and more specifically with the hypothesis that host-parasitoid interactions may constitute a major route for this phenomenon. It builds on a long- term and extensive ecological description of associations between parasitoids and their lepidopteran hosts in a natural area of Costa Rica. Through a collaboration with the University of Pennsylvania and the University of Guelph, we will sequence the full genomes of approximately 200 species from this system to assess if horizontal transfers occur preferentially between insects that are tightly connected through host-parasitoid interactions, or, in the case of Lepidoptera, through the host plants they feed on.
The project will require heavy involvement in bioinformatics and evolutionary biology concepts and methods. The ideal candidate will have a strong interest in horizontal gene transfer, and in evolutionary biology at both molecular and phenotypic levels. He or she should be at ease with bioinformatics, modeling, phylogenetic and co-phylogenetic analysis, and be inspired by the methodological challenges in these fields.
Lyon is a beautiful and lively city, not far from the Alps. The LBBE lab offers a very active scientific environment, dealing with many current issues in evolutionary biology, from molecules to ecosystems, with diverse approaches, from the bench and the field to big data and pure theory.
Applications should be submitted to Sylvain Charlat (firstname.lastname@example.org) by June 1, 2019. Please include your CV and the names of three individuals who are prepared to provide letters of reference. For further details, contact Sylvain or other team members: Julien Varaldi, Vincent Daubin, Vincent Miele, Damien de Vienne (CNRS - University of Lyon), Clement Gilbert (CNRS - Gif sur Yvette), Daniel Janzen (University of Pennsylvania), Paul Hebert (University of Guelph).
PhD Position at CNRS
We are looking for a PhD student to focus on the analysis of these experimental data. The PhD project is defined along two axes, the first one corresponding to the formalization of dynamic models, and the second one to bioinformatics analysis. This position will be based in the "Evolution of Genomes, Behavior, and Ecology" unit--a mixed-research unit in Gif sur Yvette, France.
Axis 1: Dynamic, population genetics models will describe the evolution of the number and the frequency of transposable element copies in populations. They will be based on traditional models in transposable element population genetics [9, 10], and will accommodate recently-described mechanisms (such as the epigenetic-driven regulation of transposition through small RNA, ). Models will feature stochastic phenomena (genetic drift, recombination, mutations, sampling effects), and will be used for statistical inference of parameters of interest (such as transposition rates or regulation strength) from experimental data.
Axis 2: The bioinformatics analysis will deal with the data generated by sequencing the experimental populations. The PhD candidate will have to infer new transposable element insertion sites, as well as their frequencies in populations. Standard and/or ad-hoc statistical methods (such as site frequency spectrum analysis) will then be applied in order to reconstruct the evolution and the distribution of transposable elements during genome invasion.
Required skills and training
We are looking for a student trained in bioinformatics, statistical methods, and dynamical system analysis. The PhD candidate should have basic training in computer sciences, including programming (programming languages used in our research group are R, Python, and C++). A solid experience in population genetics or evolutionary biology is also expected. Good level in written/spoken English is requested.
To learn more and apply for the position, visit the website here.
(Posted February 27, 2019)
Postdoctoral Position at Smit Lab at Institute for Systems Biology in Seattle, Washington
The lab is focused on the study of Transposable Element (TE) biology, and evolution using the latest developments in sequence modeling, phylogenetic reconstruction, and homology detection. We have developed some of the most widely used tools and databases for the study of TEs including RepeatMasker, RepeatModeler, the Repeat Protein Database, and Dfam.
The position offers an opportunity to help shape the future of the new Dfam community resource in collaboration with the Wheeler lab at the University of Montana, and through
a partnership with the NIH. The project will involve investigating and advancing de novo methods for the generation of TE libraries, development of improved methods for classifying new TE families, design of quality metrics and standards for TE modeling, providing TE family curation assistance to the research community and building/studying
TE families in a unique set of newly sequenced species.
Applicants should hold (or will shortly be awarded) a PhD degree and have experience in TE biology, and genomics. Prior experience with TE library
generation/curation, genome biology, and genome evolution are considered a major advantage. Candidates should have strong communication and data analysis skills, and
an established record of principal authorship in peer-reviewed publication(s). The successful candidate is passionate about science, motivated, proactive and able to work in
If you’re interested in joining the lab, please upload your CV with a brief description of your current research as well as 2-3 contacts for references at
https://systemsbiology.org/about/careers/. (Note that the posting is listed under the Hood-Price lab advert.)
(Posted February 25, 2019)
Postdoctoral Position at the Wadsworth Center
Laboratories of Joan Curcio and Alexey Khodjakov
A 2.5 year NSF-funded postdoctoral position is available to investigate the effects of the Ty1 retrovirus-like transposon on asymmetric cell division in Saccharomyces cerevisiae. The Curcio lab has long been interested in the relationship between retrovirus-like transposons and their eukaryotic hosts. Our recent work explores host control of Ty1 virus-like particle (VLP) assembly. Ty1 RNA is translated and packaged into VLPs in a cytoplasmic focus known as the retrosome. In collaboration with the Khodjakov lab, we have discovered that retrosome formation is asymmetrically restricted to mother cells; moreover, conditions that promote retrosome formation disrupt the age-dependent segregation of spindle pole bodies (SPBs, yeast centrosomes), a prerequisite for spindle alignment and faithful chromosome segregation. Quantitative fluorescence imaging will be used to understand how retrosome formation impacts SPB inheritance, spindle alignment, chromosome segregation and lifespan. Genetic, biochemical and quantitative imaging approaches will be combined to explore the crosstalk between the Ty1 Gag protein and SPB components as well as signaling networks that coordinately regulate retrosome formation and SPB inheritance.
Interested candidates must have a PhD or MD, strong writing, oral communication and quantitative skills, and a background in cell biology and/or genetics. Experience in retrovirus or transposon biology is a plus. Applicants should submit a cover letter, curriculum vitae, a one-page description of their research experience and goals, and the names of three or more references to joan.curcio@health.NY.gov or to:
Dr. Joan Curcio
New York State Department of Health
Center for Medical Sciences
P.O. Box 22002
Albany NY 12201-2002
(Posted October 25, 2018)
Post-Doc Associates at Danforth Center
The Slotkin laboratory is currently seeking two organized and motivated researchers to add our group. The new postdocs will investigate how transposable elements and transgenes are targeted for epigenetic silencing using cutting-edge techniques including: single-molecule long-read sequencing, whole genome methylome analysis, and small RNA deep sequencing. Both wet-bench and computational informaticists will be considered, as well as any combination of these skill-sets. Candidates with experience in epigenetics, epigenomics and/or transposable elements are highly encouraged to apply. For more information about our research program, please visit the lab page. Learn more about the position here.
PhD Studentship at Aberdeen University
This studentship aims to gain a better understanding of fundamental processes of genome evolution that remain poorly understood. The project will investigate the role of transposable elements (TEs) in evolutionary diversification following whole genome duplication (WGD), using salmonid fishes as an ideal study system due to the presence of an ancestral WGD event that has had a major impact on genome evolution and been linked with lineage diversification (e.g. Lien et al. 2016; Robertson et al. 2017). We will test the hypothesis that TEs have been instrumental agents in reshaping genetic and epigenetic evolution following WGD, promoting adaptation.
This PhD is embedded within a Norwegian research project ‘TRANSPOSE: Transposable elements as agents of genome evolution and adaptation following a recent whole genome duplication’. TRANSPOSE is a 5 year project and supervisor Macqueen is a collaborator. Position is open to UK/European applicants only. For application information, please follow the instructions on the posting here.
Postdoctoral Position at University of Texas-Austin
Postdoctoral position available for research projects investigating the mechanism of repair of phage Mu transposition and Flp recombination events by the E. coli / yeast replication machineries, respectively. This process will be explored both in vitro and in vivo using biochemical, biophysical and cell biological tools. The mechanism of Mu integration is similar to retroviruses, and we anticipate extending the studies to the repair of retroviral integration events in mammalian cells. The Flp studies have the potential for application in cancer therapy.
Applicants must have first-author publications in peer-reviewed journals and be highly motivated. A strong background in bacterial or yeast biology, DNA biochemistry, and molecular genetics is desired. Protein purification skills are a MUST. A basic understanding of programming and network analysis is a plus.
Austin, TX has been consistently ranked one of the best places to live in the United States. The University of Texas offers competitive benefits. Applicants should email their CV and list of three references to Rasika Harshey: email@example.com.
Postdoctoral Position at the NIH
Position Title: Genomic and mechanistic studies of transposable elements and HIV-1
Position Description: A postdoctoral position is available to study the mechanisms and impact of Long Terminal Repeat-retrotransposons and retroviruses. The LTR-retrotransposon Tf1 in the fission yeast Schizosaccharomyces pombe is structurally similar to retroviruses and uses mechanisms of reverse transcription and integration that are excellent models for retrovirus replication. Saturated profiles of integration sites revealed Tf1 inserts into the promoters of stress response genes. Current work focuses on how chromatin factors promote integration site selection. To identify common mechanisms of integration we generate large-scale datasets of HIV-1 integration in human cells and analyze genome-wide patterns of integration. Research is also conducted on other transposable elements to develop technology capable of generating genome-wide profiles of gene function. Further details and a list of publications can be found at:
Interested candidates must have a Ph.D. and/or an M.D. and have a strong background in molecular biology, genetics, or virology. Bioinformatic and programming skills will be of great benefit. To apply submit a cover letter, curriculum vitae, bibliography, and names of three references to:
Dr. Henry Levin
Eunice Kennedy Shriver National Institute of Child Health and Human Development
National Institutes of Health
Bld 49, room 1C32
Bethesda, MD, 20892
Employer Name: Eunice Kennedy Shriver National Institute of Child Health and Human Development
Position Location: Bethesda, MD.
The NIH is dedicated to building a diverse community in its training and employment programs.
Posted: 16th March 2017.
Bioinformatics postdoctoral position at the Evolutionary and Functional Genomics LAB, Institute of Evolutionary Biology (CSIC-UPF), Parc de Recerca Biomèdica de Barcelona, Spain.
Contact their lab for more information.