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Plant Bioinformatics Resources Workshop

  • Plant Biology 2020 Meeting
  • Wardman Park Marriott, DC
  • July 25, 2020; 10am - noon
  • Workshop web site

This workshop is intended for researchers at all levels but especially those relatively new to Plant Biology who would like to learn more about the variety of tools and resources available on the web. There will be a combination of resource overview talks and application talks which illustrate the use of specific online resources with real world examples.

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Cultivating Scientific Curiosity: Summer Workshop 2020

The BioQUEST Curriculum Consortium will host the virtual Cultivating Scientific Curiosity workshop on June 22-27, 2020. This workshop will begin with multiple hands-on sessions on the resources and tools available to develop teaching materials for your classroom. It will also provide large blocks of time for you to collaborate with colleagues and workshop staff to work on projects and to develop curriculum materials. See the Cultivating Scientific Curiosity: Summer Workshop 2020 web site on QUBES for details.

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Yeast ORFan Gene Project Summer Workshop

  • Yeast ORFan Gene Project
  • North Central College, IL
  • June 22-27, 2020
  • Workshop web site

The Yeast ORFan Gene Project is a consortium of undergraduate researchers and faculty at primarily undergraduate institutions (PUIs) to coordinate resources and design strategies to assign molecular functions to genes of unknown function in the model organism S. cerevisiae (Baker's yeast). Currently, the major activity of the network is week-long summer workshops for faculty to collaborate on adapting bioinformatic and wet-lab modules for use in classes at their home institutions. Members of the network have access to modules and protocols developed at the workshops. The 2020 workshop will be June 22-27 at North Central College, in Naperville, IL. Travel, room and board are provided for all workshop participants. The workshop application is available through the Summer Workshops section of the Yeast ORFan Gene Project web site.

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DNA Metabarcoding Workshop

  • CSHL DNA Learning Center
  • New York City College of Technology, NY
  • June 22-26, 2020
  • Workshop web site

Rather than analyzing one DNA barcode at a time, metabarcoding leverages next generation sequencing (NGS) to analyze thousands of DNA barcodes from complex mixtures of DNA—representing microbes (microbiomes) or environmental DNA (eDNA). Moving from DNA barcoding to metabarcoding perfectly embodies the conceptual transition from single gene to massively parallel genome analysis, introducing students to NGS analysis and data science. A single lane of an NGS machine can accommodate hundreds of student metabarcoding samples. Similar to DNA barcoding, metabarcoding draws on techniques from molecular biology, genetics, bioinformatics, ecology, and biodiversity. Bioinformatics analysis of metabarcoding NGS data are conducted in the recently developed DNA Subway Purple Line, a browser-based pipeline incorporating QIIME2, a research-grade metabarcoding platform.

Workshop participants learn all the biochemical and bioinformatics techniques required to implement DNA barcoding or metabarcoding, including the use of the DNALC's sequence analysis tools. Workshop seminars introduce key concepts ("big ideas"), CURE development, management and evaluation, data science, methods to work with diverse student populations, workforce development, and details about the project. Seminars include insights from project Co-PIs, including DNALC's experts; faculty leading JMU's curriculum, which engages 800 students and 20 instructors in DNA barcoding each semester; and City Tech and Bowie State faculty who lead DNA barcoding and metabarcoding with diverse student populations. The competencies required for bioinformatics, genome science, and biological data sciences are also presented.

Faculty who complete the workshops receive travel support, a stipend, and have year-round mentoring and support from project Co-PIs as they implement barcoding CUREs. Those implementing CUREs receive free reagents and DNA sequencing for student research. DNA barcoding workshop participants from the previous year are eligible to attend metabarcoding workshops—any remaining spots will be filled competitively. Select faculty will be invited to mentor other faculty, building a network of educators implementing DNA barcoding CUREs.

Faculty are asked to participate in a series of evaluation activities throughout the project, beginning with workshop evaluation. Faculty who go on to implement CUREs are enrolled in additional evaluation activities centered on their experiences as well as those of their students. Select schools will be asked to participate in additional longitudinal evaluation of students.

This workshop is free to high school and college educators, especially those in the areas of genetics, biology, genomics, and bioinformatics.

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DNA Barcoding Workshop

  • CSHL DNA Learning Center
  • Bowie State University, MD
  • June 15-19, 2020
  • Workshop web site

Just as the unique pattern of bars in a universal product code (UPC) identifies each consumer product, a "DNA barcode" is a unique pattern of DNA sequence that identifies each living thing. DNA barcoding provides a powerful way for biology faculty to lead CUREs, which have been shown to increase student retention and success when provided early in undergraduate programs. Barcoding integrates ideas from molecular biology, genetics, bioinformatics, ecology, and biodiversity - while at the same time providing the flexibility to address a variety of student-driven questions. Barcoding can be mastered in a relatively short time, allowing students to generate new data and reach a satisfying research endpoint within a single course. Furthermore, undergraduate students often have limited patience for bioinformatics, and DNA barcoding provides a wet-lab or field-based "hook" to increase engagement. Bioinformatics analysis of DNA barcodes generated via Sanger sequencing are conducted in the user-friendly DNA Subway Blue Line, an open-access, browser-based pipeline.

This workshop is free to high school and college educators, especially those in the areas of genetics, biology, genomics, and bioinformatics.

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GEP Faculty Training Workshop

  • Genomics Education Partnership
  • Washington University in St. Louis, MO
  • June 10-13, 2020
  • Workshop web site

The Genomics Education Partnership (GEP) will host a training workshop on June 10-13, 2020 for faculty members who are looking to incorporate genomics into the curriculum, and to engage undergraduate students in genomics research during the academic year. Please submit your contact information through the GEP Contact Form so that we can contact you when the registration opens later in spring 2020.

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Cell Cycle and Cancer

The goal of these multi-week activities is to use Cancer Biology as a theme to introduce concepts in the cell cycle, cell biology, genetics and signal transduction.

These activities are appropriate for high school and Introductory Biology classes.

Learning Objectives:

  1. Identify the different stages of the cell cycle.
  2. Estimate the duration of the different stages of the cell cycle from microscopic examination of onion root tips slides.
  3. Relate deficiencies in cell cycle regulation to development of cancer
  4. List the names, chromosomal location and functions of genes identified in various types of cancer
  5. Describe how mutations in cancer driver genes can result to abnormal cell biology and development of cancer cells

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Julia Ossler onto Genetics

Project Biodiversify

"Project Biodiversify provides ready-to-use examples of research concepts that highlight a diverse set of biologists.We aim to align our research examples with core biology curricula and, at the same time, highlight and humanize researchers as role models for students from many walks of life.  Our database is always growing – so check back often for updates!"

 

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Megan A. Jones onto Educational Resources

Undergraduate Research Experiences for STEM Students: Successes, Challenges, and Opportunities

"Undergraduate Research Experiences for STEM Students provides a comprehensive overview of and insights about the current and rapidly evolving types of UREs, in an effort to improve understanding of the complexity of UREs in terms of their content, their surrounding context, the diversity of the student participants, and the opportunities for learning provided by a research experience."

National Academies of Sciences, Engineering, and Medicine. 2017. Undergraduate Research Experiences for STEM Students: Successes, Challenges, and Opportunities. Washington, DC: The National Academies Press. https://doi.org/10.17226/24622.

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BioSkills Guide: Development and National Validation of a Tool for Interpreting the Vision and Change Core Competencies

Preprint of the manuscript on the development and national validation of the BioSkills Guide.

Alexa Clemmons, Jerry Timbrook, Jon Herron, Alison Crowe

doi: https://doi.org/10.1101/2020.01.11.902882

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Alexa Clemmons onto BioSkills Learning Outcomes

Synthetic genomics: a new venture to dissect genome fundamentals and engineer new functions

A nice overview of the field of synthetic genomics with a focus on future projects and the rationale for engaging in these studies.

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What is synthetic genomics anyway?

A terrific introduction to the synthesis and modification of genomes, the subfield of synthetic biology known as synthetic genomics.

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A brief history of synthetic biology

A great introduction to the history and development of the field with discussions of some of the milestone achievements.

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Foundations for Engineering Biology

An older review (2005), but still a great gentle introduction to the engineering principles that make synthetic biology distinct from other realms of biology.

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Community College Instructors' Perceptions of Constraints and Affordance Related to Teaching Quantitative Biology Skills and Concepts

A report on the survey done by the NIMBioS QB@CC Working Group.  Authored by Lisa Corwin, Stacey Kiser, Sondra LoRe, Jillian Miller and Melissa Aikens.

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Whistling Vivaldi: How stereotypes affect us and what we can do - Claude Steele

This book discusses the phenomenon of stereotype threat. It is defined as the contingency experienced by the awareness of a stereotype associated with one’s identity. This awareness research shows can result in decreased academic performance. The author includes in the later chapters very clear suggestions on teaching strategies to reduce the potential of ST in the classroom.This book discusses the phenomenon of stereotype threat. It is defined as the contingency experienced by the awareness of a stereotype associated with one’s identity. This awareness research shows can result in decreased academic performance. The author includes in the later chapters very clear suggestions on teaching strategies to reduce the potential of ST in the classroom.

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Unprofessional peer reviews disproportionately harm underrepresented groups in STEM

Unprofessional peer reviews disproportionately harm underrepresented groups in STEM

Background

Peer reviewed research is paramount to the advancement of science. Ideally, the peer review process is an unbiased, fair assessment of the scientific merit and credibility of a study; however, well-documented biases arise in all methods of peer review. Systemic biases have been shown to directly impact the outcomes of peer review, yet little is known about the downstream impacts of unprofessional reviewer comments that are shared with authors.

Methods

In an anonymous survey of international participants in science, technology, engineering, and mathematics (STEM) fields, we investigated the pervasiveness and author perceptions of long-term implications of receiving of unprofessional comments. Specifically, we assessed authors' perceptions of scientific aptitude, productivity, and career trajectory after receiving an unprofessional peer review.

Results

We show that survey respondents across four intersecting categories of gender and race/ethnicity received unprofessional peer review comments equally. However, traditionally underrepresented groups in STEM fields were most likely to perceive negative impacts on scientific aptitude, productivity, and career advancement after receiving an unprofessional peer review.

Discussion

Studies show that a negative perception of aptitude leads to lowered self-confidence, short-term disruptions in success and productivity and delays in career advancement. Therefore, our results indicate that unprofessional reviews likely have and will continue to perpetuate the gap in STEM fields for traditionally underrepresented groups in the sciences.

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Alycia Crall onto Publications

Chapter 17: Regression

test

 

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mart huisman onto 15-18

Assistant Professor of Biology (Biochemistry), SUNY Geneseo

State University of New York at Geneseo Biology Department invites applications for a tenure track Biologist (Biochemist) at the rank of Assistant Professor to begin in August 2020. The duties of the position include teaching courses at the undergraduate level, conducting research involving undergraduate students, advising students, and providing service to the department and college.

Duties include:
- Teaching a course in biochemistry as well as other biology courses
- Maintaining a research program in biochemistry that engages undergraduate students
- Academic advising
- Service to the college and community

Our priority is teaching excellence. We seek someone with a strong commitment to teaching in a liberal arts setting and who is prepared to teach both introductory courses and advanced courses in their area of expertise. A commitment to working effectively with students from diverse backgrounds is essential.

Required Qualifications: The candidate must have a PhD in a relevant discipline conferred by the time of appointment and must be qualified to teach an undergraduate course in biochemistry and additional lecture and lab courses for Biology, Neuroscience and Biochemistry majors. The candidate must have a demonstrated interest in teaching. The candidate will be expected to develop and maintain a research program in biochemistry that engages undergraduate students and can be carried out at an undergraduate institution. The candidate will be expected to maintain research productivity sufficient to publish in peer-reviewed journals and to submit grants.

Preferred Qualifications: Candidates should have experience in teaching courses and laboratories in biology and/or biochemistry. Candidates should have relevant research publications and postdoctoral research experience in biochemistry.

The successful candidate will also have demonstrated a commitment to fostering an inclusive working/teaching environment. In addition, the successful candidate will have demonstrated a commitment and ability to work effectively with a diverse group of students, faculty, staff and constituents in support of campus and department missions.

To apply, submit an online faculty application at https://jobs.geneseo.edu Applicants must upload a cover letter, a teaching portfolio with evidence of teaching effectiveness, a statement of research plans that would involve undergraduates, and a CV. In addition, applicants should be prepared to supply contact information (email address) for three references.

Review of completed applications will begin upon receipt. To be guaranteed consideration, applications must be completed by January 1, 2020.

If using Interfolio to submit letters of reference, please follow the special instructions at this link: https://www.interfolio.com/dossier/

SUNY Geneseo is an Equal Opportunity/Affirmative Action employer, committed to recruiting, supporting and fostering a diverse community of outstanding faculty, staff and students. All qualified applicants will receive consideration for employment without regard to race, color, religion, national origin, disability or protected veteran status. For our full non-discrimination statement, see: http://www.geneseo.edu/affirmativeaction.

All applicants are subject to drug and criminal background checks. See our full Background Investigation Statement at http://www.geneseo.edu/hr/employment.

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Suann Yang onto Job Postings

Desmos Graphing Calculator

Desmos produces tools that make math accessible. Their graphing calculator is compatible with screen readers, and includes audible representations of graphs. 

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Hayley Orndorf onto Tools and Resources

Accessibility Toolkit

The goal of the Accessibility Toolkit – 2nd Edition is to provide resources for each content creator, instructional designer, educational technologist, librarian, administrator, and teaching assistant to create a truly open textbook—one that is free and accessible for all students.

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Hayley Orndorf onto Tools and Resources

Needed Math

Employers, instructors of technical subjects, and mathematics educators who participated in a three-day conference on January 12-15, 2018, concluded that students’ mathematical competence should be strengthened by enhancing their ability to solve problems found in real-world contexts. The Needed Math Conference,..focused on bringing to light how mathematics education might better reflect the concepts and skills that are prerequisites for postsecondary education technical programs ... 

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Kristin Jenkins onto Developmental Mathematics

Ancient Vegetables and Fruits, with photos

This document provides links to research articles and creative commons licensed images of some ancient vegetables and fruits.   It was the basis for the display referenced in the case "A curious display."

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Margaret Waterman onto Resources for the Case Study