From 87bfce6f63d8c38102d74ef8bdf641dbbd5876df Mon Sep 17 00:00:00 2001 From: ehumph Date: Wed, 15 Feb 2023 12:57:22 -0500 Subject: [PATCH] create_information --- _site.yml | 42 ++++++++-------- bibliography.Rmd | 34 +++++++++++++ contact.Rmd | 16 +++--- index.Rmd | 45 ++++++++--------- presentations.Rmd | 84 +++++++++++++++++++++++++++++++ resources/images/ehumphries.jfif | Bin 0 -> 3870 bytes service.Rmd | 15 ++++++ teaching.Rmd | 56 +++++++++++++++++++++ training.Rmd | 33 ++++++++++++ 9 files changed, 272 insertions(+), 53 deletions(-) create mode 100644 bibliography.Rmd create mode 100644 presentations.Rmd create mode 100644 resources/images/ehumphries.jfif create mode 100644 service.Rmd create mode 100644 teaching.Rmd create mode 100644 training.Rmd diff --git a/_site.yml b/_site.yml index 02cf05a..a5ca7eb 100644 --- a/_site.yml +++ b/_site.yml @@ -1,34 +1,36 @@ -name: OTTR Template Website +name: my-website output_dir: '.' navbar: - title: OTTR Web + title: Elizabeth M. Humphries, PhD left: - text: Home href: index.html - icon: fa-home - - text: Setup - href: setup.html - - text: Hosting - href: hosting.html - - text: Editing - href: editing.html - - text: Style - href: style.html - - text: Git Actions - href: git_actions.html - - text: Docker - href: docker.html + - text: Education + href: training.html + - text: Publications + href: publications.html + - text: Teaching + href: teaching.html + - text: Service + href: service.html - text: Contact href: contact.html icon: fa-envelope + # right: + # - icon: fa-envelope fa-lg + # href: contact.html + # - icon: fa-github fa-lg + # href: http://github.com/ehumph + # - icon: fa-linkedin fa-lg + # href: https://www.linkedin.com/in/elizabeth-humphries-61202a103/ + # - icon: fa-google fa-lg + # href: https://scholar.google.com/citations?user=crSvXGoAAAAJ&hl=en + # - icon: fab fa-twitter fa-lg + # href: https://twitter.com/liz_marella output: html_document: theme: cosmo lib_dir: site_libs - self_contained: no - highlight: textmate - css: styles.css - includes: - in_header: resources/header.html + self_contained: no \ No newline at end of file diff --git a/bibliography.Rmd b/bibliography.Rmd new file mode 100644 index 0000000..db49c50 --- /dev/null +++ b/bibliography.Rmd @@ -0,0 +1,34 @@ +### +### +  +  +  +  +  + + +## First Author Publications {.tabset .tabset-fade} +  + +**Humphries, E.M.**, R.L. Kember, K. Ahn, F. Lopes, Bipolar Sequencing Consortium, P.P. Zando, F. Goes, T.I.Pollin, C. Van Hout, A.R. Shuldiner, B.D. Mitchell, M. Bucan, L.E. Hong, F. J. McMahon and S.A. Ament. In prep. “Genome-wide association study identifies novel risk loci for mood disorders in a founder population.” Target journal: Molecular Psychiatry (submitted, in review) + +Li, L., N. Liu, J.-M. Yu, **E.M. Humphries**, S. Li, B. Lindsay, Z.-J. Duan, and O. Colin Stine. 2016. “Etiology of diarrheal disease and evaluation of viral-bacterial co-infection in children under 5 years old in China: a matched case-control study.” Clin. Microbiol. Infect. 22:381.e9-381.e16. + +**Humphries, E.M.** and K. Winker. 2011. "Discord reigns among nuclear, mitochondrial, and phenotypic estimates of divergence in nine lineages of trans-Beringian birds." Molecular Ecology 20:573–558. + +**Humphries, E.M.** and K. Winker. "Working through polytomies: Auklets revisited. 2010. Molecular Phylogenetics and Evolution 54: 88-96. + +**Humphries, E.M.**, J.L. Peters, J.E. Jónsson, R. Stone, A.D. Afton, and K.E. Omland. 2009. “Genetic differentiation between sympatric and allopatric wintering populations of Snow Geese.” The Wilson Journal of Ornithology 121:730-738. + +## Additional Publications {.tabset .tabset-fade} + +N. Hasin, L.M. Riggs, T. Shekhtman, J. Ashworth, R. Lease, R.T. Oshone, **E.M. Humphries**, J.A. Badner, P.A. Thomson, D.C. Glahn, D.W. Craig, H.J. Edenberg, E.S. Gershon, F.J. McMahon, J.I. Nurnberger, P.P. Zandi, J.R. Kelsoe, J.C. Roach, T.D. Gould, S.A. Ament. 2022. "Rare variants implicate NMDA receptor signaling and cerebellar gene networks in risk for bipolar disorder." Molecular Psychiatry 27: 3842-3856. doi: 10.1038/s41380-022-01609-4 + +Kvartam M.D., et al. 2021. “Multiple dimensions of stress vs. genetic effects on depression.” Trans. Psychiatry 11: 254. doi: 10.1038/s41398-021-01369-9. + +Kalra, G., et al. 2020. “Biological insights from multi-omic analysis of 31 genomic risk loci for adult hearing difficulty.” PLOS Genetics https://doi.org/10.1371/journal.pgen.1009025 + +Peters, J.L., Y.N. Zhuravlev, I. Fefelov, **E.M. Humphries**, and K.E. Omland. 2008. “Multilocus phylogeography of a holarctic duck: colonization of North America from Eurasia by Gadwall (Anas strepera).” Evolution 62: 1469-1483. + +Gaigalas, A.K., L. Wang, K.D. Cook, and **E. Humphries**. 2004. “Photodegradation of fluorescein in solutions containing n-propyl gallate.” Journal of Physical Chemistry 108: 4378-4384. + diff --git a/contact.Rmd b/contact.Rmd index fc4eedc..86636d4 100644 --- a/contact.Rmd +++ b/contact.Rmd @@ -1,11 +1,7 @@ ---- -title: "**Contact Us**" -output: - html_document ---- +  +  +  +  +  - - -If you have questions please contact: - -* Carrie Wright (cwrigh60@jhu.edu) +You can get in touch with me by emailing me at: [ehumphri@fredhutch.org](mailto:ehumphri@fredhutch.org) diff --git a/index.Rmd b/index.Rmd index bbdd869..32f29d1 100644 --- a/index.Rmd +++ b/index.Rmd @@ -1,34 +1,33 @@ ---- -title: "**Website Name**" -output: - html_document ---- +### +### +  +  +  +  +  - +## About {.tabset .tabset-fade} +  -### **About** +Elizabeth Humphries is a postdoctoral researcher at the Fred Hutchinson Cancer Research Center. She focuses on creating data science and bioinformatics training activities for the AnVIL Cloud Computing Platform. -This website was created with the OTTR_Template_Website template. This enables simpler creation of websites that have automated checks for broken URLs and spelling errors, as well as automated rendering of all html files. No need to worry about git conflicts for html files! +```{r, echo = FALSE, fig.align='center', out.width= "20%"} +knitr::include_graphics("images//ehumphries.jfif") +``` + +You can find Elizabeth on GitHub at [ehumph](https://ehumph/). -Here is how you can include images in your website pages (this one is saved in `resources/images` to keep things tidy: -```{r, fig.align='center', fig.alt= "Example image", echo = FALSE, out.width="30%"} -knitr::include_graphics("resources/images/example_image.png") -``` - - -We will go through the following: + 
+![](http://ghchart.rshah.org/DA2536/carriewright11.svg){width=500px, } +
-1. How to set up your repository to enable the GitHub actions of the template. (Setup tab) -2. How to host your website using GitHub (Hosting tab) -3. How to modify your website structure (Structure tab) -4. How to change your website style (Style tab) -5. More information about GitHub Actions (Git Actions tab) +  +  -Click on each tab to learn more. + + \ No newline at end of file diff --git a/presentations.Rmd b/presentations.Rmd new file mode 100644 index 0000000..1e03b52 --- /dev/null +++ b/presentations.Rmd @@ -0,0 +1,84 @@ +### +### +  +  +  +  +  + + +## Presentations {.tabset .tabset-fade} +  + + +### Talks + +2022 [Informatics Technology for Cancer Research Annual Meeting 2022](https://itcr2022.org/), St. Louis, Missouri, talk titled [" ITCR Training Network (ITN) Overview](https://docs.google.com/presentation/d/1p-Mmo6mhyZVjS6ta2uZ9xqBYSPETeyiXJIC3QFkwMT4/edit?usp=sharing) + +2022 [R Medicine](https://events.linuxfoundation.org/r-medicine/), location virtual, invited talk titled ["Leveraging R for Cancer Informatics Training"](https://docs.google.com/presentation/d/15_J0CFpA22lRk2P_33CtXiYGU7tZf1fkf_OHhRHvgXc/edit?usp=sharing) + +2022 [International Chinese Statistical Association (ICSA)](https://www.icsa.org/), Gainesville, Florida, invited talk titled ["Case studies to community engagement: Bringing hands-on data science experiences to the classroom"](https://docs.google.com/presentation/d/1rN1oNZ-On4vuPanktF-HVQcS_Fr3mSqKu6pcxfwsgJI/edit?usp=sharing) + +2022 [American Association for Cancer Research (AACR)](https://www.aacr.org/meeting/aacr-annual-meeting-2022/), New Orleans, Louisiana, talk delivered with others titled ["NCI Resource: Informatics Tools and Training Opportunities +- The ITCR training network"](https://docs.google.com/presentation/d/1awxpi6dWtjc2luusgZguIZsIYxkl4LAfXHqGJ5gs08k/edit?usp=sharing) + +2022 [Current Topics in Biostatistics Research -Johns Hopkins Bloomberg School of Public Health](https://www.jhsph.edu/courses/course/33632/2021/140.860.01/current-topics-in-biostatistics-research), talk titled ["Data Science Education –A Catalyst for Change: Promoting research, community engagement, and IDARE through education initiatives"](https://docs.google.com/presentation/d/1FOIxB-pK6n24wUNSQ_yHFUGQBQP9zAUQrYAJnqh1o9c/edit#slide=id.p) + +2021 [NIH Data Science for Science Teachers Boot Camp](https://datascience.nih.gov/data-science-science-teachers-boot-camp), location virtual, talk titled ["Why Statistics Matters"](https://docs.google.com/presentation/d/1BljMC9zBp4vqqk47ecJ-cHe_6lAzqUim6IzLUoFuuKU/edit?usp=sharing) + +2020 [Bloomberg American Health Summit 2020](https://americanhealth.jhu.edu/2020-bloomberg-american-health-summit), with Stephanie Hicks, location virtual, talk titled "[Open Case Studies](https://docs.google.com/presentation/d/18jymRcaW2eh6cNmN6HbazaTg8OJFToQ28kvIpeN4CGg/edit?usp=sharing)" + +

+ +2017 World Congress on Psychiatric Genetics (WCPG), Orlando, Florida, symposium talk titled “Characterization of miRNA isoform expression in schizophrenia using human postmortem brain tissue” + +2017 Johns Hopkins Schizophrenia Center Monthly Seminar Series, symposium talk titled “Characterization of miRNA and miRNA isoform expression in schizophrenia” + +2016 World Congress on Psychiatric Genetics (WCPG), Jerusalem, Israel, symposium talk titled “Genes within the miR-137 regulation network cluster within pathways relevant for schizophrenia and related endophenotypes” + +2016 Society of Biological Psychiatry (SOBP), Atlanta, Georgia, symposium talk titled “MicroRNA 137 and its regulated genes are associated with brain imaging measures in schizophrenia” + +2014 Radboud University Medical Center and Donders Institute, Department of Human Genetics, Nijmegen, the Netherlands, oral presentation titled “Meta gene set variant enrichment analysis of miR-137 predicted and validated targets reveals schizophrenia vulnerable pathways” + +2011 Biomedical Sciences Graduate Program Student Research Day, University of New Mexico, oral presentation titled “Integration of adult-born hippocampal dentate granule cells following fetal alcohol exposure” + +2009 Biology Department Research Day, University of New Mexico, oral presentation titled“It’s always female choice - premating visual choice of female Cyprinodon rubrofluviatilis and Cyprinodon variegatus” + +2009 NIMH Career Opportunities in Research Colloquium, Albuquerque, New Mexico, oral presentation titled “Effects of ABT-239 on fetal ethanol-exposure induced learning deficits” + +### Posters + +2019 Cold Spring Harbor Biology of Genomes. Cold Spring Harbor, New York, USA, poster presentation titled "Assessment of bias and miRNA isoform quantifications of widely-used small RNA sequencing methods reveals major differences" + +2019 Small Regulatory RNAs Keystone Symposia. Daejeon, South Korea, poster presentation titled "miRNA Isoform Quantification Method Development and Expression Analysis in Schizophrenia" + +2019 Maryland Genetics, Epidemiology and Medicine (MD-GEM), Genetics Research Day. JohnsHopkins Bloomberg School of Public Health, Johns Hopkins School of Medicine, and the National Human Genome Research Institute, Baltimore, MD, USA, poster presentation titled "miRNA Isoform Quantification Method Development and Expression Analysis in Schizophrenia" + +2017 Maryland Genetics, Epidemiology and Medicine (MD-GEM), Genetics Research Day, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins School of Medicine, and the National Human Genome Research Institute, Baltimore, Maryland, poster presentation titled “Evaluation of miRNA and isomiRNA expression in schizophrenia using small RNA sequencing of postmortem dorsolateral prefrontal cortex brain tissue” + +2017 Advances in Genome Biology and Technology (AGBT), Hollywood, Florida, poster presentation titled “A benchmark test for microRNA profiling using small RNA-seq” + +2016 American College of Neuropsychopharmacology (ACNP), Hollywood, Florida, poster presentation titled “Evaluation of miRNA and isomiRNA expression in schizophrenia using small RNA sequencing of postmortem dorsolateral prefrontal cortex brain tissue” + +2016 American College of Neuropsychopharmacology (ACNP), Hollywood, Florida, poster presentation titled “Investigating expression of epistatic interaction networks in bipolar disorder in human dorsolateral prefrontal cortex” + +2016 Maryland Genetics, Epidemiology and Medicine (MD-GEM) Genetics Research Day, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins School of Medicine, and the National Human Genome Research Institute, Baltimore, Maryland, poster presentation titled “Post-mortem RNAseq characterization of the histaminergic neurotransmitter system in autism spectrum disorders” + +2015 American College of Neuropsychopharmacology (ACNP), Hollywood, Florida, poster presentation titled “Post-mortem RNAseq characterization of the histaminergic neurotransmitter system in autism spectrum disorders” + +2015 International Imaging Genetics Conference (IIGC), UC Irvine, California, poster presentation titled “Polymorphisms within microRNA-137 regulated genes together with the MIR137 risk variant, rs1625579, influence gray matter structure in schizophrenia” + +2014 International Imaging Genetics Conference (IIGC), UC Irvine, California, poster presentation titled “Meta gene set variant enrichment analysis of miR-137 predicted and validated targets reveals schizophrenia vulnerable pathways” + +2013 International Congress on Schizophrenia Research (ICOSR), Orlando, Florida, poster presentation titled “Impact of miR-137 in schizophrenia revealed by its putative targets” + +2013 Neurosciences Department Research Day, University of New Mexico, poster presentation titled “Impact of miR-137 in schizophrenia revealed by its putative targets” + +2013 Biomedical Sciences Graduate Program Student Research Day, University of New Mexico, Poster presentation titled “Grey matter effects of miR-137 putative targets involved in axonal guidance” + +2013 International Imaging Genetics Conference (IIGC), UC Irvine, California, poster presentation titled “Grey matter effects of miR-137 putative targets involved in axonal guidance” + +2011 Research Society on Alcoholism (RSA), Atlanta, Georgia, Poster presentation titled + “Integration of adult-born hippocampal dentate granule cells following fetal alcohol exposure” + +2008 Annual Biomedical Research Conference for Minority Students (ABERCAMS), Orlando, Florida, poster presentation titled “Effects of maternal drinking during pregnancy on placental gene expression and protein function” \ No newline at end of file diff --git a/resources/images/ehumphries.jfif b/resources/images/ehumphries.jfif new file mode 100644 index 0000000000000000000000000000000000000000..3f253f9b1988e51b0b262fad3a2f051a093d6a06 GIT binary patch literal 3870 zcmbW!cQhQ_n+Nb2gAtL8!6ZZU6212xA_fVfMJI??i#9qDVM3z!E=odl;$@5)eP$5C z=tH9S=)EM?`}^(LJ!k*g-S0j3`R6|Op67G!)#TM2fLcpkQyl;V0sz441-P09JOq$| zNJ&XSWY>j^jEo#iMFGAJ6o 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Baltimore + +**2018-2019** Graduate student representative to Dept of Epidemiology’s Graduate Research Committee + +**2008** Organizer, Applying to Graduate School workshop series, UAF Dept of Wildlife and Biology diff --git a/teaching.Rmd b/teaching.Rmd new file mode 100644 index 0000000..e9b2b55 --- /dev/null +++ b/teaching.Rmd @@ -0,0 +1,56 @@ +### +### +  + +## Teaching {.tabset .tabset-fade} +  + + +### Instruction + +**2017-2022** Adjunct Instructor (online course: Molecular Phylogenetics Techniques), [Johns Hopkins Advanced Academic Programs](https://advanced.jhu.edu/) + +**Fall 2018, 2019** Guest lecturer, [University of Maryland Baltimore GPILS core course](https://lifesciences.umaryland.edu/) (Professor: Dr. Michelle Giglio) + +**2012-2014** Adjunct Professor (course: Biology I), [Reading Area Community College](https://www.racc.edu/) + +**2012** Adjunct Professor (courses: Biology for Non-Majors, Human Health and Disease), [Harford Community College](https://www.harford.edu/) + +**2010** Intructor (course: Genetics), [UAF Alaska Summer Research Academy](https://www.uaf.edu/asra/) + +**2009) Intructor (course: Introduction to Molecular Biology), [Rural Alaska Honors Institute](https://www.uaf.edu/rahi/) + +**2001-2004** Tutor, [UMBC Chemistry Tutorial Center](https://chemistry.umbc.edu/overview/chemistry-tutorial-center/), Student Director Fall 2004 + +**Summer 2002, 2003** Instructor, UMBC Summer Chemistry Workshop, [Meyerhoff Program](https://meyerhoff.umbc.edu/) + + +### Courses and Activities Developed + +**2022** [GDSCN: SARS Phylogeny on AnVIL](LINK), a module using RStudio for college undergraduates + +**2022** [Molecular Phylogentic Techniques](LINK), a course on basic phylogenetics analyses for MD students + +**2022** [Statistics for Genomics: PCA](LINK), a module introducing MS graduate students to common statistical analyses + +**2022** [Statistics for Genomics:scRNA-seq], a module introducing MS graduate students to common statistical analyses + +**2020** SIR Models and Outbreaks, an activity for late elementary students on modeling disease outbreaks in a population + +**2010** Jurassic Genetics, an activity for the Alaska Summer Research Academy using the concept of cloning extinct organisms to introduce students to the basic tenets of genetics and molecular biology to middle and high school students + +**2009** Introduction to Molecular Biology, a course for the Rural Alaska Honors Institute introducing advanced high school students to both basic and advanced topics in genetics, molecular biology and evolution, as well as train students to do molecular biology and genetics research + +**2009** The Poisoners: A Molecular Murder Mystery, an activity to help high school students students review different types of molecular methods and reinforce what information can be gained from using each method as they attempt to solve the murder of Dr. Splicer + + +### Mentorship + +**2020-2021** University of Maryland Baltimore, Shelvonne Burton (undergraduate student), Meghann Ryan (graduate rotation student), and Jayme Choe (MS student) + +**2007-2009** University of Alaska Museum Department of Ornithology, Tim Sanner (HS senior) and Cyndie Beale (HS teacher) + + + + + diff --git a/training.Rmd b/training.Rmd new file mode 100644 index 0000000..7301c08 --- /dev/null +++ b/training.Rmd @@ -0,0 +1,33 @@ +### +### +  +  +  +  +  + +## Training/Education{.tabset .tabset-fade} +  + +### Postdoctoral Training +  + +Dr. Humphries is currently a postdoctoral researcher with the [AnVIL Project](https://anvilproject.org/) under the guidance of [Dr. Jeff Leek](https://jtleek.com/) and [Dr. Ava Hoffman](https://www.avahoffman.com/). She creates training content for the AnVIL platform. + +Dr. Leek is the Chief Data Officer, Vice President, and J Orin Edson Foundation Chair of Biostatistics at the [Fred Hutchinson Cancer Center](https://www.fredhutch.org/). Dr. Hoffman is a Senior Staff Scientist with the [Fred Hutch Data Science Lab](https://hutchdatascience.org/). + + +  + +### Doctoral Work + +  + +Dr. Humphries earned her PhD in [Epidemiology](https://www.medschool.umaryland.edu/epidemiology/) from the [University of Maryland Baltimore](https://www.umaryland.edu/) in December 2021. She focused on molecular and genetic epidemiology. + +Dr. Humphries's graduate work was performed at the [University of Maryland Baltimore Institute of Genome Sciences](https://www.igs.umaryland.edu/) under the guidance of [Dr. Seth Ament](https://www.medschool.umaryland.edu/profiles/Seth-Ament/), an expert in psychiatric genomics and neuroscience. + + +### Masters Work + +Dr. Humphries was awarded her Masters in [Biology](https://www.uaf.edu/bw/) from the [University of Alaska Fairbanks](https://www.uaf.edu/) in December 2008. She studied genetic variation in Beringian birds. Her advisor was Dr. Kevin Winker, the curator of ornithology at the [University of Alaska Museum](https://www.uaf.edu/museum/collections/bird/). \ No newline at end of file