Happy Summer!
I hope everyone’s been enjoying the summer heat that’s apparently been sweeping the country (and the world)! Even SF is getting “hotter” at a nice 21-22°C. Though down around Stanford it’s closer to 29°C… which is why I don’t go there too much.
For July, both Jessica and I have been getting a ton of work done! While she’s been wrangling protocols and prepping the lab for more phage work, I’ve been helping her build a spreadsheet-based research assistant tool.
My research assistant tool currently does things like search Pubmed and can “ask AI” the same question across 100+ papers — e.g. “what phage purification methods were used”.
It also creates better summaries and abstracts based on papers’ discussion and methods sections. Oh, and as a bonus — it can translate any journal article into any language — like Japanese or Spanish — and then read the entire article in that language.
I’ll do a longer write-up next week on how both Jess and I use my research assistant tool! And we’ll slowly roll it out to everyone in the next few weeks.
(If you want quicker access, email me at [email protected])
~ Jan
Here’s what we’ve covered this month:
by Bishoy Maher Zaki
In this article, Bishoy discussed his journey from phage isolation to bioinformatics, highlighting his current efforts to streamline phage genome analysis tools for the research community. He emphasized the importance of collaboration within the phage bioinformatics community and launched a survey to gather input on preferred tools, aiming to create a comprehensive resource for researchers — if you have a chance, please fill out his survey!
Additionally, the article addressed urgent requests for specific phages needed for patients in the UK and Belgium, showcasing the ongoing need for phage therapy in clinical settings.
by Jan Zheng, Jessica Sacher
This month’s Phage Picks were a treasure trove of exciting research!
I highlighted an article on how AI has transformed protein science, hinting at the future of computational biology in the phage field. This is a slight departure from previous Picks as it’s not a phage journal article, but I feel is very important for the field nonetheless.
Jess shared an in-depth protocol from the Israeli Phage Therapy Center, detailing their comprehensive approach to phage therapy, which she found particularly inspiring.
We also explored a high-throughput method for detecting and characterizing phages, a study on mobile genetic elements in bacterial immunity, and a paper discussing a phage tail-like bacteriocin that could lead to targeted antimicrobials.
I think the phage field has really been hitting its stride in the last year, and there’s so many great papers getting published every week.
by Jessica Sacher
In this article, Jessica explored the distinctions between n of 1 clinical trials and compassionate use in the context of phage therapy. She reflected on her initial confusion regarding the two concepts, noting that while compassionate use aims to provide unapproved treatments to patients in need, n of 1 trials are structured clinical studies where a single patient serves as their own control.
She then highlighted the challenges of applying n of 1 trials to phage therapy, particularly due to the complexities of bacterial infections and treatment interactions. She also mentioned a recent n of 1 trial conducted in Canada, expressing interest in learning more about its design and outcomes.
To wrap up the article, Jess wondered whether n of 1 trials could offer a viable alternative to traditional clinical trials in the phage therapy landscape, especially given the difficulties in recruiting sufficient patients for larger studies.
C&T Throwback!
Since Jessica’s been up to her neck in phage production protocols, I thought it’d be nice to re-read Kyle Jackson’s post on how JAFRAL does phage production consistently and repeatably.
