SEA-PHAGES Logo

The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

The SEA-PHAGES Program

SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester, discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses, but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses.

The program aims to increase undergraduate interest and retention in the biological sciences through immediate immersion in authentic, valuable, yet accessible research. By finding and naming their own bacteriophages, students develop a sense of project ownership and have a ready-made personal research project at a fraction of the cost of traditional apprentice-based research programs. Some of the positive effects of the SEA-PHAGES program have been reported here.

SEA-PHAGES is jointly administered by Graham Hatfull's group at the University of Pittsburgh and the Howard Hughes Medical Institute's Science Education division.

SEA-PHAGES IN THE NEWS

  • Thumbnail for  Steele commended by Nobel Prize winner for her work

    Steele commended by Nobel Prize winner for her work

    Barbara Phillips

    Archer County News | April 21, 2016

    It is not often that a freshman in college is approached and commended for research by a Nobel Prize winner, but that is exactly what happened to Archer City graduate, London Steele, now a freshman at Baylor University....read more

    Related institution: Baylor University

  • Thumbnail for Queens University student discovers a virus strain

    Queens University student discovers a virus strain

    Reid Creager

    The Charlotte Observer | April 16, 2016

    Sydney Dishman’s new pet isn’t cute and certainly isn’t something you’d want to cuddle with. But she feels good just thinking about it. Her “pet” is named Rex16, after the Queens University of Charlotte mascot and her year of graduation. Rex16 is a bacteriophage species she discovered while completing her honors research thesis, investigating bacteriophages in local soil samples....read more

    Related institution: Queens University of Charlotte

  • Thumbnail for Students in interactive course look to discover, name phages

    Students in interactive course look to discover, name phages

    Marlon Morgan

    Western Carolina News | Sept. 30, 2015

    Western Carolina University student Sean Kent didn’t pick the course, but when he saw he was registered for it, the name “Phage Hunters” immediately got his attention. Brooke Burns also found she was placed in the course. After hearing so many other freshmen at orientation say they were excited about WCU’s newest biology/chemistry course, she, too, decided to keep it. Now she says it’s by far her favorite....read more

    Related institution: Western Carolina University

  • Thumbnail for Biology 2.0

    Biology 2.0

    Andrea Gaul

    Baylor Arts & Sciences Magazine | May 9, 2017

    Baylor University has implemented a new kind of introductory biology lab that has proven successful in keeping students excited and engaged through hands-on research.read more

    Related institution: Baylor University

  • Thumbnail for One student gets to name lab discovery

    One student gets to name lab discovery

    Oscar Santiago Torres

    Eagle News | Aug. 27, 2014

    An agar plate lies still. Omnicron has destroyed the layer of bacteria inside the plate, leaving plaques or dark holes 2 mm in diameter. Omnicron is a virus replicating itself inside the plate. The discovery of this virus belongs to Tasha Baer, a Florida Gulf Coast University student from the 2013-14 Virus Hunters course....read more

    Related institution: Florida Gulf Coast University

  • Thumbnail for UWF Biology And Chemistry Crews Team Up To Hunt Phages

    UWF Biology And Chemistry Crews Team Up To Hunt Phages

    Bob Barrett

    wuwf 88.1 | May 12, 2015

    The University of West Florida has been chosen to pioneer a unique collaboration between its chemistry and biology departments. Let’s start off with an important definition....read more

    Related institution: University of West Florida

  • Thumbnail for A summer of sequencing

    A summer of sequencing

    Joseph McClain

    Ideation | Sept. 6, 2013

    It was the summer that the freshmen ruled the sequencer. Technically, the six William & Mary students who logged heavy lab time with a state-of-the-art Ion Torrent gene sequencer had finished their freshman year and therefore did their summer work as rising sophomores....read more

    Related institution: College of William & Mary

  • Thumbnail for Del Mar student takes home award for research on bacteriophages

    Del Mar student takes home award for research on bacteriophages

    Fares Sabawi

    Corpus Christi Caller Times | March 29, 2016

    Before John Ramirez, 29, decided to go back to school, he worked at Northwest Hospital in Calallen. There, he saw how tuberculosis affected people. "It's almost intensified when you see it," Ramirez said....read more

    Related institution: Del Mar College

  • Thumbnail for This scientific paper has 2,863 authors. How?

    This scientific paper has 2,863 authors. How?

    Danielle Wiener-Bronner

    Fusion | May 12, 2015

    The scientific journal eLife published a paper on viruses last month—specifically, the genetics of bacteriophages: viruses that infect, and replicate within, bacteria. By sequencing the genomes of individual bacteriophages, or phages, the authors were able to glean information about the genetic makeup of the viruses more broadly.... read more

  • Thumbnail for Student ‘Virus Hunters’ publish research in peer journal

    Student ‘Virus Hunters’ publish research in peer journal

    FGCU 360 | July 2, 2015

    Students and faculty involved in FGCU’s “Honors Virus Hunters” course helped produce a research paper that has been accepted for publication in eLife, a highly ranked peer-reviewed scientific journal for the biomedical and life sciences....read more

    Related institution: Florida Gulf Coast University

  • Thumbnail for Round Rock Cedar Ridge grad earns scientific honor

    Round Rock Cedar Ridge grad earns scientific honor

    Mike Schoeffel

    Austin American-Statesman | Feb. 28, 2017

    Isabel Delwel, a junior at the University of North Texas, was chosen to participate in the 2017 Howard Hughes Medical Institute Exceptional Research Opportunities Program. One of Delwel’s professor’s, Dr. Lee Hughes, encouraged Delwel to apply for a spot in the program.read more

    Related institution: University of North Texas

  • Research paper with 2,863 authors expands knowledge of bacteriophages

    Science Daily | May 11, 2015

    We know that bacteriophages are viruses that infect and replicate within bacteria. We know that they are the most abundant organisms on Earth. But we don't know much about their genetic architecture....read more

    Related institution: University of Pittsburgh

  • Thumbnail for WKU 2012 Goldwater Scholarship Recipient Charles Coomer

    WKU 2012 Goldwater Scholarship Recipient Charles Coomer

    innovateKY/YouTube | April 24, 2012

    Charles Coomer, a junior in the Honors College at WKU and the son of Evell and Don Coomer, has been involved in microbiological research for two years. In the lab of Dr. Rodney King, associate professor of biology, Coomer is characterizing viruses that infect bacterial cells...read more

    Related institution: Western Kentucky University

  • Thumbnail for Biology major chosen for research at MIT

    Biology major chosen for research at MIT

    Drew Sterwald

    FGCU 360 | June 2, 2016

    Santiago Yori already has research experience under his belt that most biology majors would envy. But he’s taking it to a new level this summer working alongside scientists at the Massachusetts Institute of Technology. A veteran of FGCU’s elite Honors “Virus Hunters”...read more

    Related institution: Florida Gulf Coast University

  • Thumbnail for Freshman find

    Freshman find

    Kyrie O'Connor

    Houston Chronicle | Oct. 15, 2016

    Brian Blake Maxfeldt likes science just fine, but he didn't go to college expecting to make a discovery his first year. Nevertheless, Maxfeldt, who goes by Blake and graduated from Morton Ranch High School in Katy, discovered a virus that nobody had ever seen before.read more

    Related institution: LeTourneau University

Abstract Submission for 2017 Symposium

Dear SEA Faculty Members,

We are excited that the 2017 SEA Symposium is rapidly approaching. Below is information regarding abstract submission for the SEA Symposium (Cohort 10 excluded).

Who Should Submit an Abstract?

  • Each school with student participant(s) for the 2017 SEA Symposium is expected to submit one scientific abstract about bacteriophage work accomplished by students this year. This abstract should be presented during the poster session by the students attending the symposium. One poster space will be set aside for each participating school.
  • Each school may also submit a second abstract, to be presented by the attending faculty. Due to space restriction, a limited number of these posters will be selected for presentation at the poster session.
  • As you submit each abstract, please indicate if you would like your abstract to be considered for a talk. Each of these abstracts will be reviewed and considered for a 12-minute talk. Note that abstracts selected to for a talk will also be expected to be presented at the poster session.
  • Please also note that you will need to upload a photo (headshot) for each of the poster presenters when submitting an abstract.

Abstract Guidelines

  • Abstract titles can be up to 200 characters long.
  • Abstract body text can be up to 3,000 characters long.

Poster Guidelines

  • Note that even if your abstract is selected for a talk, you will also present a poster.
  • The final poster dimensions must fit into an area no larger than 4’ x 4’.
  • The poster heading should include a title, names of authors, and the name of your institution.

How to Submit an Abstract

To submit an abstract for the meeting, you must be a verified SEA-PHAGES faculty member, and you must log in to seaphages.org. After doing so, you can use the link in this timeline to submit an abstract. Alternatively, go to your institution's page and follow the link found there: https://seaphages.org/abstracts/submit/22/ .

When to Submit an Abstract

The abstract is due by Friday, May 5, 2017.

Keep in touch with the most up-to-date information on the upcoming Symposium on the meeting page.

Email us at info@seaphages.org if you have any questions.

The SEA-PHAGES Team

Annotation Forum Reorganization

An Inherent Problem with Annotation

With the constant influx of new software tools, new genomes, and new publications, the way we annotate genomes is always changing. We always know a bit more than we did last year, and often a lot more than we did 5 years ago.

This leads to an inherent problem, however, in that we only officially train SEA-PHAGES faculty once, and obviously Cohorts 1-8 were trained more than one year ago. In addition, the genome you worked on at the Bioinformatics Workshop may be nothing like the genome you're currently annotating, and you'll inevitably come across new and puzzling regions.

Before? No...After? No...During!

The question is, how can we share what we've learned with the whole SEA in a manner that helps you do the most up-to-date annotations possible? We can put out "What's New?" documents before you begin annotating, which we do, but these often only cover broad strokes rather than details. Or we can provide feedback after you've submitted your final annotation, which we also do, but these details can be easily forgotten over the summer before you tuck into your next genome, and may not apply if you have a different cluster phage anyway.

Therefore, to our mind, the best time to get feedback is while you're actively annotating your genomes. And while we love answering questions about the cool and interesting things you're finding, we'd like that answer to be shared with everyone who might be coming across something similar so we don't end up have to answer it many times over!

Which obviously brings us to the seaphages.org Annotation Forum, where we can give specific, real-time feedback in a manner that's visible to others who might have similar questions. Therefore, we strongly encourage you to use the forum for questions you've come across while annotating.

Reorganization of the Forum

Which brings me to the point: I've slightly rearranged the Annotation Forum and renamed/clarified/broken up some of the existing threads to try to make everything more transparent and useful. Within the main annotation forum, there are now specific sub-forums for questions about calling start sites, calling functions, getting the notes right, and more. Please go ahead and ask questions in any of these. Here are a few quick pointers...

  • Post specific titles to your questions, like "Large gap in a Cluster F1 phage" or "Write NKF or leave blank in minimal notes?" This will help others find answers more than titles like "Question about two genes".
  • On each thread, try to keep the discussion specific to that topic. So if someone asks a question about the difference between a hydrolase and an esterase, don't use that same thread to ask about the HHPred cutoff for a hydrolase. Instead, create a new topic.
  • The Annotation Forums are public, which means students can use them as well. And their PhagesDB logins will also work on seaphages.org.

Happy annotating!

The GO Annotation Competition is upon us!

If you are annotating phage genomes in Spring, you might be interested in an exciting inter-campus Gene Ontology (GO) annotation competition devoted to phage genomes and hosted by Texas A&M University. Last year, 5 SEA-PHAGES campuses joined the competition.

GO annotations are formal statements about the function/role/location of a gene product (e.g. protein X has glucosidase activity or protein Y is part of the phage tail baseplate). As part of the competition, students have to find literature sources providing experimental evidence of a given function/role/location for a phage gene product and enter the annotation using the wiki-based interface. These annotations can be challenged and corrected by students from other campuses and instructors, and students must revise them to earn full credit. Once completed, annotations are submitted to the GO repository for everybody to see and use.

Performing GO annotations in a competitive setting is a great way to have students read, parse and distill a scientific manuscript into the elementary units of knowledge it contributes. If you are interested in participating, please contact Steve Caruso (scaruso@umbc.edu) or Ivan Erill (erill@umbc.edu) of UMBC for more information. They have abundant training material to share with you.

Upcoming Events

9th Annual SEA-PHAGES Symposium

June 9, 2017 to June 11, 2017

2017 Genome Announcement Workshop

June 11, 2017 to June 13, 2017

Phage Discovery Workshop Option A

June 24, 2017 to June 30, 2017

Recent Events

2017 Symposium Abstracts Due

May 5, 2017

Forum Activity

jparker posted in New HHPred web site

Veronique Delesalle posted in Terminase vs DNA packaging

Jacqueline Washington posted in HAD superfamily hydrolalse

FORUMS HOME PAGE