@lskatz

Public health bioinformatics scientist at CDC. ♥ programming. Podcaster. Proud former TOAST team lead. Statements here are my only voice and not of my employer.

 Atlanta, GA
about.me/lskatz
Joined May 2008
  • Tweets1.5K
  • Following363
  • Followers829
79Media
>Hi tweeps! @andrewjpage, @happy_khan, and I have been working on the podcasting idea for the last several months, and it is finally coming to fruition! Please take a look at quadram.ac.uk/micro-bioinfor… and like and subscribe!

New podcast for microbial bioinformatics community

Dr Andrew Page and Dr Nabil-Fareed Alikhan from the Quadram Institute and Dr Lee Katz from the Centers for Disease Control and Prevention have produced the Micro Binfie Podcast for scientists, researc

quadram.ac.uk
3
8
3
40
Mashpit 🤘 sketching out genomic epidemiology joss.theoj.org/papers/10.211… 🧬🖥️🧪 github.com/tongzhouxu/mashpi…
1
8
910
The backstory behind the FASTA bioinformatics format youtu.be/7LA0IKsVloU?si=KNg8… via @YouTube
3
21
2
111
14,196
My kids keep asking me to play Bacteria in car rides. It is especially cute coming from a three year old demanding "bacteria." I think I have been playing #riskyornot too often rofl @bugcounter @benjaminchapman
1
4
191
And then when they're demanding bacteria, I can't go into the episode. I have to start from the beginning and then rewind when the intro ends.
124
🚀 Exciting News! Our new tool primerForge just got published! 🎉 🔬 primerForge compares two groups of genomes to identify PCR targets—making it easier to distinguish pathogens in infectious disease outbreaks. 🦠 Check out the paper by Joe Wirth et al.👇 joss.theoj.org/papers/10.211…

primerForge: a Python program for identifying primer pairs capable of distinguishing groups of...

Wirth et al., (2024). primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other. Journal of Open Source Software, 9(101), 6850, https://...

joss.theoj.org
2
17
771
We're back with @microbinfie! @happy_khan and I talk about tree visualization at on.soundcloud.com/S6veFuffex… or wherever you get podcasts
1
4
144
We need a 25th amendment but for justices. Let the circuit judges remove the corrupt justices if Congress won't.
2
135
That's no laughing matter. This is why the Chevron doctrine was so important. We need real experts tackling today’s complicated problems, not judges who think they know better.
This quoted post is unavailable.
Try viewing anyway · View on X
88
1,014
28
2,150
92,125
Next time you see Trump, ask him who he's voting for.
1
115
After rewriting WFA-go, the speed reaches 1/10 of the official C++ version🫣, with 3X memory. It's production-ready, please try it. A binary is also provided to align seqs in cmd-line. I also wrote the dev notes which might be useful for other developers. github.com/shenwei356/wfa

GitHub - shenwei356/wfa: Wavefront alignment algorithm (WFA) in Golang

Wavefront alignment algorithm (WFA) in Golang. Contribute to shenwei356/wfa development by creating an account on GitHub.

github.com
1
16
41
5,703
AMD academy 2024 kicked off today! Looking forward to a week of bioinformatics and discussion of strategies for lab and epi collaboration! Starting off strong with @lskatz lecture on sequence quality! @CDC_AMD @APHL
2
3
13
525
Funding opportunity from CDC. There are several different topics especially related to bioinformatics, genomics, and metagenomics. sam.gov/opp/d01f45cdc73545a9…
1
3
531
💡 Ready to level up your bioinformatics game? Fasten is here to help! This toolkit offers a seamless solution for fastq file operations. Simplify your workflow and focus on what matters – your research! #Bioinformatics 🚀 fosstodon.org/@joss/11191844…

JOSS (@[email protected])

Just published in JOSS: 'Fasten: a toolkit for streaming operations on fastq files' https://doi.org/10.21105/joss.06030

fosstodon.org
3
7
531
@RustRepos
76
@lskatz, @den_bakker and @jhphan
118
Proud of our work
CDC Advanced Molecular Detection@CDC_AMD
26 Dec 2023
Using whole genome sequencing & a Reference Identification Database, scientists can identify bacteria that are most associated with foodborne illnesses. See how they determine these species in a new article from @FrontMicrobiol: bit.ly/3RlG5ev #AMD #PublicHealth
Public health scientist analyzing whole genome sequencing data.

ALT Public health scientist analyzing whole genome sequencing data.

9
371
Using whole genome sequencing & a Reference Identification Database, scientists can identify bacteria that are most associated with foodborne illnesses. See how they determine these species in a new article from @FrontMicrobiol: bit.ly/3RlG5ev #AMD #PublicHealth
Public health scientist analyzing whole genome sequencing data.

ALT Public health scientist analyzing whole genome sequencing data.

3
1
11
1,742
Interested in single-cell data, brain, and evolution? Postdoc position available in the Soojin Yi lab (at UC Santa Barbara). Genomic data analysis experience required (Python/R, databases). recruit.ap.ucsb.edu/JPF02653
1
20
34
6,977
Jurassic park 🦖is 30 years old & the science 🧬 is still relevant. For a bit of fun @happy_khan @lskatz & I watched it & comment on all the #science in the movie! 🎙️ soundcloud.com/microbinfie/r… #JurassicPark
1
4
1
17
1,630
Guess what I don't see on these @netflix results? 👎
189
Load more