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Seth Shipman Profile
Seth Shipman

@seth_shipman

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scientist. shipman lab at gladstone | UCSF.

San Francisco, CA
Joined July 2008
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@seth_shipman
Seth Shipman
28 days
Heema Selvakumar, @vivek_mutalik:.A. baylyi (0.2%). Jee-Hwan Oh, Jan-Peter van Pijkeren:.L. reuteri (0.1%). Laura Bonillo-Lopez, Virginia Aragón:.S. suis (0.1%). Ching-Chung Ko, Graham Hatfull:.M. smegmatis (6%). @NastassiaKn, Marc Güell:.C. acnes (0.02%).
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@seth_shipman
Seth Shipman
28 days
@alex_gonzadel: .C. freundii (22%).K. pneumoniae (22%).P. aeruginosa (7%). @_miloj, @bkoskella:.E. amylovora (4%).P. syringae (0.7%) . Michael Wold, @bacteriality: .V. natrigens (45%).A. hidrophyla (26%). @YLekbach, Zihan Yu, @KeitzLab: .S. oneidensis (98%).P. putida (0.2%).
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@seth_shipman
Seth Shipman
28 days
Everyone ran the editing in their own favorite species. Of the 15 species (incl E. coli) we found editing above 20% in six of them, above 40% in three of them, and above 90% in two of them. New species and collaborators follow with retron recombineering editing rates:.
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@seth_shipman
Seth Shipman
28 days
New Preprint!! @alex_gonzadel accomplished a major feat on this one: ported retron recombineering, which we love so much in E. coli, into 14 new bacterial species via a massive collaborative effort involving 9 labs!.
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@seth_shipman
Seth Shipman
30 days
RT @NatureBiotech: The June issue is live On the cover, Khan et al. present a molecular census of retrons, perform….
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@seth_shipman
Seth Shipman
6 months
There aren't too many natural retron hosts around, so if you're interested in researching retrons in their real context, let me know and we'll be happy to share these hosts.
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@seth_shipman
Seth Shipman
6 months
Kazuo Nakamura went out and collected bacteria and, with @thekarenzhang and @matromont, found and characterized the retrons in the lab. @pentamorfico helped us understand a weird retron system that had not previously been described.
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@seth_shipman
Seth Shipman
6 months
We just posted a new preprint where we found retrons in bacteria out in the real world, in dirt and water. We describe the first retrons in a handful of new species, show how they defend against phages, and use them to edit genomes. Read about it here:
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@seth_shipman
Seth Shipman
7 months
Now published @NAR_Open! SspA is a transcriptional regulator of CRISPR adaptation in E. coli.
@seth_shipman
Seth Shipman
1 year
New preprint from the lab, on the fundamental biology of CRISPR adaptation! Check out the preprint here: Or, start with this wonderful highlight thread by @oso_de_antojos who led the work. @GladstoneInst @UCSF @UCSF_BTS @BioE_Beast.
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@seth_shipman
Seth Shipman
7 months
Congrats, Kate! We'll miss you! Supporting roles on this one from @Asim_g_Khan, @oso_de_antojos, and @genophoria. Institutional support: @GladstoneInst, @UCSF, @BioE_Beast, @UCSF_BTS. Funding: @NSF, @NIBIBgov, Keck Foundation, @pewtrusts.
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@seth_shipman
Seth Shipman
7 months
🚨New Pub: High throughput variant libraries and machine learning yield design rules for retron gene editors, now out in @NAR_Open. This is a great one, and the last bit of @katecrawdaddy's PhD, who is off to David Bakar's Lab for a postdoc.
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@seth_shipman
Seth Shipman
10 months
RT @claudiasjv7: 🚨 Episode 6 of #FromBenchtoPodcast is live! 🎙️👩🏻‍🔬 Tune in as @ChloeFishman and I dive into the fascinating world of #Phag….
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@seth_shipman
Seth Shipman
10 months
RT @GladstoneInst: Gladstone scientists undertake a major effort to examine the diversity of retrons, bacterial defense systems that can be….
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@seth_shipman
Seth Shipman
10 months
RT @NatureBiotech: An experimental census of retrons for DNA production and genome editing
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@seth_shipman
Seth Shipman
10 months
Here's the SharedIt link for free access to the paper: Great job on this one @Asim_g_Khan @matromont @alex_gonzadel @oso_de_antojos @callmeRebeccaF @katecrawdaddy, and institutional support @GladstoneInst @UCSF @UCSF_BTS.
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@seth_shipman
Seth Shipman
10 months
An experimental census of retrons, now published in @NatureBiotech. We synthesized more than a hundred new retrons and put them through their paces, improved recombineering rates and precise editing in human cells up to 40%.
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@seth_shipman
Seth Shipman
10 months
RT @jeffnivala: Published today in @Nature, we describe an approach for single-molecule protein reading on @nanopore arrays. By utilizing C….
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@seth_shipman
Seth Shipman
10 months
RT @SorekLab: A new retron-based method from the innovative @seth_shipman lab now allows making multiple mutations in a phage genome in a s….
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@seth_shipman
Seth Shipman
10 months
Here's the SharedIt link to the article that is free to access:
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@seth_shipman
Seth Shipman
10 months
Implications explained and a peek behind the scenes with this fantastic article from @GladstoneInst .
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