Jan Zheng, MHCI
I'm Jan, the other half of Phage Directory, and co-write Capsid & Tail.
Previously, I did data work at Phage Australia / Westmead Institute, where I built the biobank databases, data systems, and bioinformatics workflows for the clinical trial
I have a background in computer science and human-computer interaction, and I'm currently full-time at building the agentic layer for science at Nvidia.
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- Our Phage Picks for Aug 2025 It’s Phage Picks time! This week, we highlight some new mind-expanding papers — one showing how phage killing might train the immune system like vaccines, one unpacking how temperate phages rewrite bacterial flagella with RNA-guided tools,…
- C&T Round Up for July 2025! This month, we explored how Canada's first successful prosthetic joint infection phage therapy case is leading up to a full clinical trial; plus Jessica wrote a guide/manifesto(?) about why you should sequence (and re-sequence) your phages.
- C&T Round Up for June 2025! This month, Jess went viral with a post about How to Read Papers, we picked some great bread and butter papers, and Jess got to chat with Cytophage about navigating the Canadian regulatory phage maze.
- C&T Round Up for May 2025! For this month, we feature a guest post about pipolin use in PCR, two podcasts from Jess, and another lab hacks episode from Jan.
- Finding papers at scale Among the millions of papers published each year, how can you make sure you never touch another irrelevant paper?
- C&T Round Up for April 2025! Another round up! This month, we feature a new Lab Hacks format from Jess, one of our most controversial Capsid posts on AI use in science, and a Phage Picks of some of Jessica's nearest and dearest protocols (she uses these all the time —…
- Our Phage Picks for April 2025 It's Phage Picks time! This week's theme is bread and butter — two picks from Jess about methods papers that should be staples of any phage lab: her favourite phage-making paper, and an (aspirational) phage quantification paper she really…
- C&T Round Up for March 2025! Roundup time! This month, we heard from Aaryan's experience as an undergrad researcher at Paul Bollyky's lab. We picked papers across topics like T4-AAV viral vectors, cell-free synthesis of phages, and taxMyPhage, a new tool for…
- Our Phage Picks for March 2025 What else can phages do, besides kill bacteria? Are bacteria even needed to make them anymore? In this month's Phage Picks issue, we cover phage+AAV hybrids to deliver genes to eukaryotic cells, cell-free phage synthesis, and a bonus…
- C&T Round Up for February 2025! Issue #300! This month we announced the return of Evergreen, covered Intralytix's 25-year-long overnight success, and Silvia's journey to build up a new phage lab.
- The Year of the Phage Machine Happy 2025 everyone! It's still January so we can still say happy new year! We are finally back after a nice long extended Christmas break + insanity January. Tons of phage news has accumulated — here you go!
- Year in Review 2024 This year we moved from Sydney to San Francisco — what a year. Here's some reflections, things that went well, things that didn't, and some things we learned. Happy holidays to everyone!
- C&T Round Up for November 2024! Roundup time! This month we explored phage therapy at Mayo Clinic with Dr. Gina Suh, Yamini Patel shared her experience at the VoM 2024 Conference in Australia, and Esme Brinsden discussed a new citizen science initiative in South England.…
- C&T Round Up for October 2024! Roundup time! This month we explored phage-based gene editing in the microbiome, high schooler Kate Kelly shared her jam-packed 30 days in Stanford’s Bollyky lab, and Ritah Nakayinga from Kyambogo University discussed her phage cocktail to…
- Our Phage Picks for October 2024! It's Phage Picks time! This week we've got the seventh rendition of our new format, where we share the papers we keep bookmarked, and keep coming back to.
- C&T Round Up for September 2024! This month we heard about how Sartorius' columns can bring down endotoxins close to zero. There's also a new phage data resource called Phage Base! Lastly, we also picked a couple of super interesting papers this month — one about how…
- Our Phage Picks for September 2024! It's Phage Picks time! This week we've got the sixth rendition of our new format, where we share the papers we keep bookmarked, and keep coming back to.
- Can AI extract data from a messy spreadsheet? What if we could instantly extract information we need from a spreadsheet (like raw plate reader data) in just a click? Can AI help? This week, Jan writes about a project he worked on for Sphinx Bio, where he tried to extract data from…
- C&T Round Up for July 2024! This month, we recap what we learned about phage genome analysis tools, phage production pipelines, n of 1 clinical trials, and more!
- Our Phage Picks for July 2024! It's Phage Picks time! This week we've got the fifth rendition of our new format, where we share the papers we keep bookmarked, and keep coming back to.
- C&T Round Up for June 2024! For this month, we found some super interesting phage papers, heard about phage-vectored vaccine production, and more!
- Our Phage Picks for June 2024! It's Phage Picks time! This week we've got the fourth rendition of our new format (and Jan's favourite..!) where we share the papers we keep bookmarked, and keep coming back to.
(Yes, Jan now reads more phage papers than Jessica, and she's…
- C&T Round Up for May 2024! Round up time! This month we covered why phage researchers are flocking to Australia in July (and California in June!), discussed our 'phage picks' for this month, and shared a very special story from one of the researchers that make up the…
- Our Phage Picks for May 2024! Here's the third rendition of our new format: Phage Picks — where we share the papers we keep bookmarked... and keep coming back to.
- C&T Round Up for April 2024! Round up time! This month we covered phages and neutrophils, reflected on Phage Directory and Phage Australia, and did our second 'Phage Picks' issue.
- Our Phage Picks for April 2024! Here's the second rendition of our new format: Phage Picks — where we share the papers we keep bookmarked... and keep coming back to.
- C&T Round Up for March 2024! Round up time! This month we did our first 'Phage Picks' issue, dove into how prophages impact fly sperm, shared insights and recordings from Urmi's webinar series with top phage therapy clinicians, and Elisabet More from PDB Biotech taught…
- Our Phage Picks for March 2024! We're starting off the year by trying a new format: Phage Picks — where we share the papers we keep bookmarked... and keep coming back to.
- Year in Review 2023 This week we wrap up 2023 and reflect on our biggest surprises and proudest moments! Things are also changing in 2024...
- Experimenting with REDCap This week, we introduce a new mini-series about building experiments on REDCap, a tool used for collecting clinical patient data. In the first issue, we dive deep into building instruments with nested permutations.
- C&T Round Up for November 2023! Round up time! This month Jan released Open Phage Data Sheet (google sheet full of phage tools/links/resources, open to all to contribute!) and shared a walkthrough on using ChatGPT for data work. And Libby Duignan wrote about her recent…
- AI-Assisted Data Engineering This week, we share some examples and learnings from experimenting with data processing and extraction using OpenAI’s slew of new ChatGPT tools!
- Introducing the Open Phage Data Sheet This week we’re launching Open Phage, a public, editable spreadsheet of phage resources like grants, clinical trials, and bioinformatics/lab tools!
- C&T Round Up for October 2023! This month, we heard about the Southeast Asia phage workshop, a few tidbits from Evergreen, and a brief intro on using ChatGPT for lab work!
- ChatGPT tips for lab work This week, we get to explore and share some ideas about how to (responsibly) use ChatGPT for lab work!
- Evergreen 2023: Looking Back This week, we finally get to post the recap of Evergreen Phage Meeting! With a flurry of guest posts, we didn't even get to write about Evergreen until a couple of months after the event — but here's what went down, a picture gallery, and…
- C&T Round Up for September 2023! This month we heard about the ICBRAR phage conference in India, got an excerpt from The Good Virus by Tom Ireland, had a look behind the scenes of a Swiss team battling UTIs with engineered phages, and learned about speeding up the phage…
- The Good Virus: A book about phages by Tom Ireland This week we're featuring an excerpt from a new book about phages, called The Good Virus.
- Evergreen 2023 Schedule & Lineup! Hi everyone! Evergreen is in TWO DAYS! We’re doing a lot of work preparing for the 25th Evergreen Phage Meeting, and it’s been a whirlwind. There’s a lot we’ve done, and there’s a lot left to do for before, during, and after the meeting.…
- C&T Round Up for July 2023! This month, we heard about PHIOGEN, a new phage startup, about how the phage therapy system works at Phage Australia, and about a biobank data platform we're building at Phage Australia.
- Proof & Provenance: A biobank data platform for coordinating and sharing phages and results How do you design a system that can share data across phage labs and biobanks? But also track where a phage came from and where a phage went? And along the way let each lab selectively pitch in their lab data? We'll get into some higher…
- C&T Round Up for June 2023! This month, we really put the CAPS lock in Capsid: from ORACLE to a CARB-X article on SNIPR, to AKTA and DBs, we really capitalized on many deep topics.
- Working with data in biology This week, Jan starts to apply ideas from the previous Data series to the world of biology work and biology data.
- C&T Round Up for May 2023! This month, we covered a new phage podcast, launched the Evergreen Phage Meeting sign up site, and talked about using databases for phage work!
- Working with Databases This week, Jan continues his casual "Data Series" of posts to show how phage labs can start using relational databases today, with Airtable.
- Evergreen turns 50: celebrating Dr. Betty Kutter’s legacy This week, we’re proud to open up registration for the Evergreen Phage Meeting. This year’s Evergreen phage meeting will be in-person (!), absolutely packed with science and activities (!!), and will be a celebration of both Betty’s…
- C&T Round Up for April 2023! This month, we talked about analyzing qPCR results, Phage Australia's official response to the Phage UK inquiry, and got hands on with building a project with ChatGPT!
- Phage Australia responds to UK Parliament’s phage inquiry This week, we look at some highlights from a white paper that Phage Australia published as a response to the UK Parliament Inquiry on phage therapy.
- C&T Round Up for March 2023! This month we featured a new phage startup out of Shanghai, and massive write-ups on lab automation, working with tabular data, and using qPCR for phage therapy.
- Working with tabular data This week, Jan takes another detour into data-land, playing around with spreadsheets and tabular data, exploring VLOOKUP, pivot tables, and other formulas.
- C&T Round Up for February 2023! This month, we featured a new UK Phage Therapy initiative and wrote about lessons in scaling bio and how to think about data.
- How to think about data This week, Jan goes meta about data. Everyone throws around the term data, but what is it exactly? Jan explores the different kinds of data, how to work with data, and shares some ideas for keeping data neat and tidy.
- C&T Round Up for January 2023! This month, we wrote an article for GARDP about phage therapy business models. For this issue, we're also revisiting a couple of gems from Dr. Paul Jaschke's lab!
- 2023: A look ahead Well hello there, 2023! We’ve made great strides in the past year, gotten our hands wet in the lab (Jessica at least 😉), built data systems, and even delivered phages for patients. This year we aim to do a whole lot more of that! This…
- Reflecting back on 2022 We’re at the end of the year again, and what a whirlwind of a 2022 it’s been! Here's our annual end-of-year reflection on what we're most proud of, what we've accomplished, & those who've helped us along the way!
- On Data Analytics and Biology This week, Jan takes a detour into data analytics! This follows up on the last informal Data Series post designing an auditable, replicable, and accessible phage data system. This time, Jan delves a bit deeper into what data analytics is,…
- C&T Round Up for November 2022! Happy December, everyone. I hope you've all enjoyed your Thanksgiving! Jessica and I took a short break in New Zealand and it was sublime. This past month, we featured an article by Adam Yang that explored COVID-19 and phages. We also…
- C&T Round Up for October 2022! This week, we highlight our October feature articles: Dive down the rabbit hole with us on designing phage data systems, building sustainable phage therapy, and get excited for this year's World Phage Week!
- How to design a phage data system This week Jan Zheng explores a few design decisions and considerations behind building a system for collecting data from every part of the phage therapy pipeline.
- MetaPhage: Towards user-friendly phage bioinformatics MetaPhage is a new pipeline for turning raw reads into phage insights. It’s a massive step in the right direction towards one-click phage analysis. Here's my trying (and failing) to run MetaPhage on a laptop, and a short tutorial to get you…
- Spot or Not: A simple system to rate your spot tests How do you turn subjective observations into a quantified, somewhat-less-subjective observations? This week Jan Zheng continues his phage data series, delving into how (and why) the well-known 'Net Promotor Score' used by software companies…
- How to organize your biobank data Now that we’ve covered tracking phage metadata and building identities for our phages, it’s time to consider how our phages fit into our biobanks. This week in Capsid and Tail, Jan Zheng explains his thinking on how to organize phage…
- How to name a phage What's in a phage name, and how can we make it count? Should we give phages pet names or serial numbers? This week Jan Zheng continues his informal blog series on phage data, with a new post on how he's thinking about naming phages.
- How to keep track of phages As your phage collection grows, keeping track of your phages and associated data becomes increasingly important. This week, Jan Zheng explores how to rein in all that data before it gets out of control.
- 2022: Building the Operating System for Phage Therapy Good morning, 2022! We’re extremely proud of our work empowering the community, running events like Evergreen and building Instill. This year, we'll be focused on building the “operating system” for phage therapy. From lab workflows to web…
- Reflecting back on 2021 It's our last issue of the year! We reflect on what we're especially proud of from this year, and highlight some stats on where we're at as a community!
Also: a giant thanks to each of our amazing volunteers!
- State of Phage #3: Exploring phage collections We're compiling the results of our State of Phage 2020 Survey, and we're excited to show you a third snapshot of the findings! Today we're focusing on phage collections; which phages are labs collecting, how many do they have of each, and…
- Evergreen 2021: Many thanks to all 504 phage phans! Last week, in collaboration with Dr. Betty Kutter and her unstoppable team, we helped run the iconic Evergreen International Phage Meeting — but with a twist — this time it was a hybrid virtual/in-person event! We are overjoyed with how it…
- Raise your impact with Instill Science Are your manuscripts meeting their potential? We're launching a new community initiative called Instill Science to help you raise your impact (and get credit for helping your fellow phage community members do the same).
- Phage Futures Congress 2021: Meeting Recap We attended Kisaco Research's Phage Futures Congress 2021 at the end of February, and now present our recap of the event. We hope to provide a window into what you missed, and/or a refresher if you were there!
- State of Phage #2: A wide diversity of strains We're compiling the results of our State of Phage 2020 Survey, and we're excited to show you a second snapshot of the findings! Today we're focusing on strain collections; which bacterial species are phage labs collecting, how many do they…
- State of Phage #1: A wide diversity of backgrounds & phage experience It's been almost three months since we launched our State of Phage 2020 Survey! We're excited to show you a snapshot of the data coming in. Today we're focusing on who responded to the survey: where are they from, what's their career stage,…
- 2021: Empowering the phage community Hello 2021!! This year, we're focusing on empowering the phage community with the knowledge and tools it needs to overcome phage research challenges & help others do the same.
- Looking back on the year 2020 For our last issue of 2020, we're reflecting back on Phage Directory's 2020 progress, and the incredible collaborators who have made it possible. We're really proud of the ways we've been able to connect and work with the phage community…
- Creating a searchable directory of phages We're excited to share a sneak-peek into our progress toward creating a global phage catalogue and search tool!
- Phage Futures Congress 2020: Meeting Recap The last time we were at a conference, it was Phage Futures Congress 2020 (Feb 5-6, 2020). Since we're all working from home, it's a perfect time to reflect back on the phage development community's recent progress.
- Apply for Phage Directory-VoM Writing Awards! Attention student and postdoctoral phage biologists planning to attend Viruses of Microbes 2020 in Portugal this year! Phage Directory will be sponsoring two cash awards in collaboration with the Viruses of Microbes organizing committee,…
- Online communities and working from home In the spirit of social distancing and working from home, this week we're exploring some ideas and tools that enable online communities and allow teams to collaborate from around the world and to work from home.
- Capsids in the classroom (and a challenge for 2019) This week, we’re sharing insights from our experience talking to middle school kids about phages, phage therapy, and Phage Directory.
- Tweaking the microbiome with phages: Q&A with BiomX CBO Assaf Oron This week, we bring you a Q&A with BiomX CBO Assaf Oron.