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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 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 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 First-years discover viruses, analyze DNA

    First-years discover viruses, analyze DNA

    Kate Nussenbaum

    The Brown Daily Herald | Feb. 10, 2012

    Sixteen first-years watched with excitement as their screens loaded the sequence of 59,625 nucleic acids that comprise the DNA of “Job42,” the virus a student in their class had discovered, isolated and named during the fall semester. “Each of them codes for something,” said Jordan Rego...read more

    Related institution: Brown University

  • 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 Freshmen participate in huge research study on tiny viruses

    Freshmen participate in huge research study on tiny viruses

    CU Boulder Today | May 1, 2015

    A new study appearing this week in the scientific journal eLIFE about the rapid evolution of small viruses that infect bacteria includes 59 University of Colorado Boulder co-authors, all of whom conducted research for the paper as freshmen....read more

    Related institution: University of Colorado at Boulder

  • 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 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

  • 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 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 Young Māori scientist discovers virus

    Young Māori scientist discovers virus

    Rukuwai Tipene-Allen

    Māori Television | April 22, 2018

    Young, Māori scientist Anezka Hoskins has discovered a new virus and is hopeful that it will spark curiosity amongst Māori to push boundaries of knowledge.read more

    Related institution: Massey University

  • Thumbnail for La Sierra freshmen discover new viruses through national research program

    La Sierra freshmen discover new viruses through national research program

    Darla Martin Tucker

    La Sierra News | June 15, 2017

    La Sierra University freshman Casey Jang was pleasantly surprised—she knew it was possible, but really didn’t expect to find, and then name, a virus that is new to science.read more

    Related institution: La Sierra 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 Bio major considered dream come true for department

    Bio major considered dream come true for department

    Melanie Greenberg

    Loquitor—Cabrini College Student Media | March 5, 2011

    Surrounded by only her thoughts and glass beekers, one Cabrini student spends much of her time diligently working in the Iadarola Science Center. Katie Mageeney, senior biology major and math and chemistry minor, is anything but an average student. “Katie is definitely dedicated to her lab work,”...read more

    Related institutions: Cabrini University | Lehigh University

  • Thumbnail for Durham Tech students present research at national symposium

    Durham Tech students present research at national symposium

    Charlton Budd

    Chapelboro.com | June 27, 2016

    Two Durham Tech students were given the chance to present their research at a national symposium earlier this month. Qina Mo and Peter Said presented their research describing the isolation and characterization of two viruses that infect bacteria at the 8th annual SEA-PHAGES Symposium...read more

    Related institution: Durham Technical Community College

  • 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

Fall 2019 Faculty Hack-A-Thons

What is it?

 

The Fall Faculty Hack-A-Thons is a series of one-day annotation workshops for faculty that are hosted by our SEA-PHAGES SMART Team and expedited submitters. The goal of the Hack-A-Thons are to improve faculty annotation skills across the SEA and help everyone refresh their memories before they teach the bioinformatics component in the Spring. These small group, faculty-focused workshops will either work through the annotation of one genome from the genome exchange or will focus on a particular annotation topic. Along the way, faculty will be reoriented to SEA-PHAGES bioinformatics tools, the Online Guide, annotation submission guidelines, changes from previous years, and useful forums and resources on seaphages.org.

 

Who should attend?

 

We encourage all faculty that will be leading the bioinformatics course to attend at least one of these workshops. Teaching assistants are welcome if there is space. Cohort 12 faculty will soon attend a week-long in-depth bioinformatics training workshop. There will be some hack-a-thon sessions available as follow up for Cohort 12 trainees, but it’s not recommended to attend a Hack-A-Thon until after the workshop.

 

How to attend one?

 

These workshops will take place as in-person meetings, virtual meetings, or a combination of both. To attend one of these meetings, refer to the sign-up link below, which lists all the dates and locations for these meetings. Once all faculty have identified their top three choices, you will be contacted with additional details about the meetings. Food will be provided at in-person meetings, but travel to and from a meeting is at your own expense.

 

Please identify up to three workshops that you can attend, and rank your preference, by Sunday Oct 20, 2019.

 

Sign-up here: https://www.surveymonkey.com/r/2019FallHackathon

 

Happy Annotating!

 

The SEA-PHAGES Team

Sequencing Status 2019-2020

Below is a live spreadsheet showing the status of SEA-PHAGES sequencing samples for the 2019-20 academic year. Generally, only samples in the "priority" queue will be listed, and it may take a few days after receipt of samples for them to appear.

CLICK HERE to open this in a new browser window.

 

2019 SEA-PHAGES Annual Letter

The 2019 SEA-PHAGES letter is available in pdf format by clicking here, or you can read the text below.

Dear SEA-PHAGES Community,

The 2019 SEA-PHAGES Annual Symposium marks yet another highly successful year with a plethora of exciting events. The program continues to expand with inclusion of a new cohort of schools and we are especially pleased to welcome the Cohort 12 faculty to the Symposium. We are delighted to share with you a few of the highlights from the past year.

2018-19 Program Highlights and Accomplishments

  • Program Growth and Milestones

This fall, we will welcome 18 new institutions into the SEA-PHAGES program as Cohort 12. Included among these are our first schools from Arizona, New Hampshire, and Canada, as well as a second institution in Puerto Rico. Geographical diversity is great, but phage diversity is even better, so Cohort 12 will be trained using Arthrobacter globiformis and Gordonia rubripertincta as hosts. And SEA-PHAGES schools now represent 43 different US states, as well as the District of Columbia and Puerto Rico. 

Because of our collective efforts, we will soon pass 3,000 sequenced Actinobacteriophage genomes, and nearly 2,500 of those genomes are published in GenBank. We reached 2,000 sequenced genomes in May 2017, so we are now finding and sequencing the genomes of nearly 500 novel phages per year, which is a tremendous accomplishment and rich collection and data set. And there are now five genera on which we’ve isolated and sequenced at least 200 genomes: Mycobacterium, Arthrobacter, Gordonia, Microbacterium, and Streptomyces. Thank you for all your work in making this happen!

  • Mycobacteriophage therapy

One of the most exciting scientific developments over the past year culminated in the publication of a paper in Nature Medicine this May describing the use of a phage cocktail to treat a disseminated drug-resistant Mycobacterial infection in Isabelle Holdaway, a British 15-year-old with cystic fibrosis who had received a lung transplant. After receiving the three-phage cocktail—which contained two BRED-engineered phages—Isabelle showed substantial health improvement, and the story received international media attention. One of the three phages used, ZoeJ, was found by a SEA-PHAGES student at Providence College, but many of your SEA-PHAGES phages were screened to find the few that were useful.

The primary scientific goals of SEA-PHAGES are to understand the basic principles of phage diversity, but this development illustrates a key point: that translational applications depend on and emerge from basic scientific exploration. It is hard to imagine how this life-saving intervention could have occurred without the SEA-PHAGES program.

  • Microbiology Resource Announcements

In June 2017, we held a Genome Announcement Workshop where we encouraged SEA-PHAGES faculty members to learn to write and submit papers describing the phage genomes they’d found. The seed planted at that workshop has begun to bloom, as the past year has seen at least 12 Microbiology Resource Announcements on which (non-Pitt) SEA-PHAGES faculty members are the corresponding authors. Congratulations!

  • Future Symposia, Faculty Meetings, and Workshops

If you’re from one of the earlier SEA-PHAGES cohorts, you probably remember when you could bring a faculty member and two students to the Symposium each year.  But the growth of the program has bumped up against the capacity of Janelia Research Campus, and we’ve had to moderate the number of attendees per institution to fit everyone. In the interests of long-term sustainability, therefore, the 2020 Symposium will be held at a new location, the National Conference Center in nearby Leesburg, VA. This facility has been carefully vetted and should provide an excellent location and atmosphere to accommodate our ever-growing group of student researchers and faculty members.

Each year, immediately following the Symposium, we hold another meeting for faculty only. In even-numbered years, this is a full faculty meeting where one representative from each institution is invited, and in odd-numbered years it is a specialized workshop of some sort, where invitations are based on the topic covered in the workshop. This year we are hosting a Microbacterium Phage Genomics workshop, whereas next year will be a full faculty meeting.

  • Removing Annotation Bottlenecks

With nearly 500 genomes being sequenced each year, the task of getting high-quality annotations into GenBank in a timely fashion has grown. This past year saw a number of developments that aimed to remove some of the bottlenecks in the annotation pipeline.

First, the June 2018 full SEA-PHAGES faculty meeting focused on improving the quality of phage genome annotations and bringing everyone up to speed with the current best practices. There were lots of “aha” moments and many genomes were submitted directly to GenBank as a result of the meeting.

Second, the number of expedited submitters has grown to include 50 SEA-PHAGES faculty members representing 39 institutions. Expedited submitters use a streamlined submission form and their genomes go quickly into GenBank, easing the QC burden. We thank those of you who have worked to achieve this status and hope to add many more this coming year.

Third, a sustained effort from a dedicated team at Pitt allowed us to completely clear out the pile of genomes awaiting QC in early 2019. We have new plans in place to make sure your genomes are processed as expeditiously as possible in the future, and your adherence with the annotation deadlines will help to make this a reality!

We will continue to improve this pipeline in ways that it is helpful to you. This will include an online file-checker that will allow you to identify and fix any issue with your submission files before entering them in PhagesDB, and will avoid them being returned to you for common errors. Watch out for announcements soon!

  • Feedback

We are always interested in hearing your feedback, suggestions, concerns, and questions about the larger aspects of the SEA-PHAGES program’s direction. We’ve created a new forum called “Larger Program Questions” and encourage you to share items there.

Thanks for being part of this vibrant and productive community. Wishing all of you a successful and fun year, and we look forward to seeing you at the Symposium.

Sincerely,

David Asai and Graham Hatfull

Upcoming Events

Philly Phage Phestival - 2019

November 16, 2019

Bioinformatics Workshop

December 9, 2019 to December 13, 2019

2018 Bioinformatics Workshop

December 9, 2019 to December 13, 2019

Recent Events

Phall Phage Phair - 2019

November 8, 2019

Virtual Site-Visit with SEA Team

September 1, 2019 to October 31, 2019

Forum Activity