Jonathan Jacobs 🧬🦠🕹️🏕️
@bioinformer
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Authenticity and data provenance in #genomics + #bioinformatics . Also #scicom , @officialATCC #gaming #DnD #EDM #punk @ Home ♟👾🎮 🎸he/him
US & elsewhere
Joined April 2011
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5,048 genomes! 4,224 bacteria, 451 viruses, 359 fungi, and 4 protists. 1,649 type-strains.
This is an important milestone at the ATCC Genome Portal. When I joined the team in 2019 - we had a goal of hitting 5,000 authenticated microbial genomes by 2025, and we’ve passed that
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This is one of my favorite (over simplified) ways of explaining PCA analysis to to non-stats people.
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5K
Fun
#Bioinformatics
facts:
1/ FASTA was (is) a software package for searching DNA sequences.
2/ the “FASTA” input file format was never intended to be a standard,
3/ the common 80 character width of FASTA files are due to the resolution of DEC VT220 terminals in the 1980’s. 💾
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I think a lot of people think
#bioinformatics
is something like this. 🧐😏 and it sort of is… 😂
#weekendreading
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@dgonzales1990
I get this all the time too for people trying to contact…
1/ the _other_ JJ who work in microbial genomics at UCLA or
2/ the other JJ that works on MicroBiome of plants root systems, or
3/ the other JJ who is a Baptist minister
4/ the other JJ who is a genealogist
3 out of 4
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All the major public
#genomics
databases have intentionally falsified data in them but researchers either don’t care, don’t think it will affect them, or don’t believe genomic misinformation is a problem.
What unpopular academia opinion would get you in this situation?
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If this resonates with you, come work with us.
(Yes this is a sub tweet)🫣😉
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Happy to announce I'll be joining
@ASMicrobiology
's
@JournalSpectrum
as an Editor!🥳focusing on microbial
#genomics
,
#metagenomics
,
#bioinformatics
, and related omics' topics. Hopefully I won't do too much damage... 😂 (kidding!) 🧬🦠🧫 Looking forward to helping.
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We’re about to open up another Senior Bioinformatician position (MSc +3-5yrs; or recent PhD) on my team - so if you’re keen to live in the DC area, like building pipelines, playing with code, and have a passion for
#genomics
standards and authentication of data - send me a DM 🧬
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Over 3,500 authenticated microbial genomes are currently available on the ATCC Genome Portal () - reference genomes for 3,205 bacteria, 254 fungi, 293 viruses, and 4 protists so far. Over 100+ released every month too! :) 🧬🦠🍄🚀
#genomics
#bioinformatics
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If you are interested in having your
microbes sequenced for free,
simply have them accessioned at ATCC. Chat me up for details.
We're doing
@illumina
/
@nanopore
hybrid WGS for the entire
@officialATCC
collection. Check our progress:
#ASMicrobe
#genomcis
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So let me get this straight -
#MAGA
supporters were previously denying
#COVID19
, made mask wearing a political issue (🙄), are now saying that people participating in the
#GeorgeFloyd
#BlackLivesMatter
protests are putting America at risk becuase of
#COVID19
? Hmmmm...
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34720 fungi
16135 bacteria
2215 protists
1295 viruses
this is the number of strains in ATCC's microbial collection that have never been sequenced before ... by anyone
... looks like we'll be busy for quite a while with the ATCC Genome Portal
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A short story about
#bioinformatics
,
#genomics
, bacterial reference
#standards
and the challenges and complexity of doing reproducible science. (Names changed to protect the innocent! ☺)
🧬🧬👍👍
A thread...
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Did you know that you can have whole genome sequencing done (for free) on your microbial strains?
Just:
1/ deposit your microbe
@officialATCC
2/ have it accessioned into the General Collection
3/ data released via ATCC Genome Portal
Requests here:
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Q: When was the first time falsified sequence data was submitted to GenBank?
A: 1997
Q: Is the data still in GenBank even though it was part of a ORI investigation and cited in the Federal Register as being falsified?
A: Yes.
Q: Is the data labeled as being falsified?
A: No.
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Did you know that if you deposit and accession your bacteria, virus, or fungi into the collection at ATCC, we'll do whole genome sequencing, assembly, and annotation as part of our QC and accessioning?
#WorldMicrobeForum
cc:
@officialATCC
@ATCCgenomics
#genomics
#bioinformatics
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Direct from today’s group meeting… (in reference to discussing another group’s whole genome assemblies…) 😉🧬🦠
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Q for
#bioinformatics
and
#genomics
community :
Who coined the term “read” or “reads” when referring to an individual sequencing result?
And when? (Refs / citations welcome)
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Join my team! 3 new positions at all levels now open (more coming too) as we continue to expand both the genomics (wet) lab and
#bioinformatics
sides of my group
@officialATCC
. Interested in a
#biotech
job in
#genomics
? Speak 🧬WGS, 👩💻RNAseq or 😎 databases? See🧵for details👇
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Massive impostor syndrome because I was “trained” by my post doc advisor that industry scientists were hacks and sellouts - but what I encountered were some of the most baddass scientists I’d ever worked with. Was not prepared for that.
PhDs working in industry:
What "culture shocks" did you experience during your first 6 months in an industry role?
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IDEA:
@discord
community for
#bioinformatics
collaboration, training, mentoring, news, etc.
Networking for academics, gov, and industry.
Real-names only. No anonymous alias BS like on Reddit.
Hackathons, perhaps quarterly.
Seminars monthly.
Journal clubs perhaps weekly or
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Interested in automated library prep for
@Nanopore
sequencing?
We just updated our protocol for our
@Eppendorf_USA
#EPMotion
5075. Now it's "fully walk away and combines both the end-prep and barcode ligation." check it out >
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I love this paper so much for so many reasons.
Dayhoff, M. O. “Computer Analysis of Protein Evolution.” Scientific American 221, no. 1 (July 1969): 86–95.
Note the date.
And omg the figures.
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"To consult a statistician after an experiment is finished is often merely to ask him to conduct a post-mortem examination. He can perhaps say what the experiment died of." - RA Fisher (1938)
If will need a bioinformatician after the experiment, don't wait - talk to them today.
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Reproducibility in RNAseq 🧵 - so, i've been playing around with
#RNAseq
data from original/unmodified HEK293 cells taken from a variety of studies in SRA (in black). Our cells (colored) are also parental HEK293 and one derivative HEK293 cell line. Notice how close even our
ahhhh... no wonder... 🤦♂️
"Hundreds of cancer papers mention cell lines that don’t seem to exist"
#cancer
#research
#Integrity
#cellbiology
#oncology
#science
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Looking forward to today’s poster session - Day 3
@ASMicrobiology
’s
#ASMicrobe
! 🦠🧬🦠🥳
Come by at 10AM or 4pm and let’s chat about
#genomics
and
#bioinformatics
in microbiology! Poster MBP1268. 😊
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Wow! Just learned we’re about to release a 5S/16S/23S rRNA removal kit for bacterial
#RNAseq
. Wish I had this 3y ago! Saves 1.5h+ & drops >95% rRNAs from sample. Interested? Chat w/Brian Dugan
#ASMicrobe
@QIAGEN
Booth 1033
#microbiome
#metagenomics
#metatranscriptomics
#genomics
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If there's one thing i've learned - if anything - after 20+ years in
#bioinformatics
is that if someone has already solved a problem, developed a solution, or released software, and it's still being maintained, then 99% of the time it's not a good idea to try to also solve it.
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Back in 2013, I started maintaining a GoogleDoc of published
#metagenomics
pipelines.
By 2018, 100+ pipelines existed, so I stopped
Today: ~180+ pipelines _just_ for taxonomic profiling of shotgun data…😐
What are you using for your metagenomics / microbiome analysis?
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If you're looking for authenticated ref genomes for microbes - check out the 3,329 assemblies my team at
@officialATCC
has produced.😁💪🧬😉
We're presenting an update at
#BioITWorld
this week too, so DM me for a meet up!
#genomics
#bioinformatics
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Hey
#RNAseq
folks... what's up with this volcano plot?🌋🧬N=4/condition. Human cells.
Ever seen "wings" like this before?
#Looksodd2me
- but raw data looks great. qPCR confirmed DEGs. Maybe rounding/precision error in pipeline? Maybe I just worry too much?
#bioinformatics
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35 days since manuscript submission and our paper is still with the editor.
This isn't a criticism of the editor - becuase I know they are working on getting reviewers to sign up.
it is though a criticism of how peer review is breaking.
People just don't want to sign up.
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Playing
#wordle
on Super Expert mode.
WORDLE: "Guess a 32 letter word!"
@Illumina
: "acetNNNlactosa" and "saminyltrNNNferases"
@Nanopore
: "aceNNylgalctsamNnyltraNNferases"
@PacBio
: "acetylgalactosNminyltransferas"
@iontorrent
: "aaacetttylgaaaa"
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Is it just me - or is this one the many "Elephants in the Room" for
#bioinformatics
and
#genomics
?
... 🤔😐😭😂🦠🧬🚀
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Someone sent me an example of a Manhattan plot used in a GWAS study... 👀 seems legit...
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It occurred to me today that I think it may now cost more and take longer to publish a novel microbial genome in a peer reviewed journal than it does to actually sequence, assemble, annotate, and compare it vs it’s nearest neighbors🤔🧬🧐
#genomics
#Bioinformatics
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New publication highlighting the ongoing work in my group
@officialATCC
to produce authenticated reference genomes for our entire collection of fungi, bacteria, and viruses.
#genomics
#bioinformatics
Current total is 4,100+ actually. 😊
🧬🦠🧫🔬
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This beauty came up in journal club today... and we now have a potential reason why we missed it last year when searching for "complete genome"s of Acinetobacter - we apparently needed to also search for "cpmplete genomes" 🤦♂️(cc:
@NCBI
)
#genomics
#qualityassurance
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If microbial
#genomics
,
#dataprovenance
and reference genome quality matters to you, then you might want to check out our new
#bioinformatics
paper
@biorxivpreprint
☺🦠🧬🚀
Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies
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At
@nanopore
’s pathogen event -
@laura_boykin
urges the global
#publichealth
community to stop doing “labs in a suitcase” and colonial science, but instead focus on building local in country infrastructure and jobs.
#ASMicrobe
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We sequenced 9 species last month which had no genome reference previously available.
P. halophilus
S. gopherii
Tatumella terrea (2!)
Proteiniphilum sp. TSD267
B. andersonii
P. pogonae
B. durdenii
H. maura
Sorry, but I just this think is so cool!🚀🦠🧬
#Genomics
Wow!🤩 The ATCC Genome Portal now has 3,118 authenticated microbial reference genomes!
What's new?
+169 bacteria
+3 fungi
+2 viruses
Likely our biggest monthly update ever!
#genomics
#bioinformatics
#microbiology
#ILoveMyJob
cc:
@officialatcc
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Great
#genomics
epidemiology talk from Dr
@iruka_okeke
on Antimicrobial Resistance in Africa. So much data! I❤️this!
#AMR
#publichealth
#asmicrobe
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😱Nearly 4K!💪
The ATCC Genome Portal now has 3,821 authenticated microbial reference genomes!! All produced in-house by my team
@officialATCC
! Over 95% are super accurate hybrid-assemblies from
@Illumina
+
@nanopore
#NGS
#genomics
#bioinformatics
🚀🧬🦠
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I’ve started a new public List for independent
#Bioinformatics
#Consultants
who are on
@Twitter
. If you are one or know one - please reply here and I’ll add to the list.
Everyone else in
#genomics
: please retweet this. Could be useful to many people
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just completed
@Nanopore
R9 vs. R10 for 48 different bacteria... identical workflows, only diff was R10 flowcell v14 chemistry
honestly rather underwhelmed
base calling much higher, but...
fewer & shorter reads, lower throughput
no difference in hybrid assembly quality
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Mad props for
@DrKatHolt
@JuddLmj
@rrwick
latest!💪🧬🦠
Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing
Nearly all the microbial genomes at the ATCC Genome Portal are Illumina/ONT hybrids - so this resonates!
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Five positions open on my team at ATCC (!!)
😱🧬☣🦠😂
If you want to join a growing
#genomics
lab and
#bioinformatics
team at
@OfficialATCC
> check it out! > 3x Biologist, 1x Senior Biocuration Specialist, and a Scientist (Biomedical Genomics) position☺
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Hey
#ASMicrobe
- interested in authenticated reference genomes for microbiology, virology or mycology?
The ATCC Genome Portal is a growing db of 3,300+ genomes from
@officialATCC
. Stop by MBP11-655 or DM me to learn more!
🎉🧬🦠
#genomics
#Bioinformatics
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My teenage son was in a head on collision today.
Both cars totaled.
Fortunately everyone walked away.
No major injuries.
No concussions.
Shaken up? yes.
Taking the rest of the day off? Yes.
Hats off to the engineers and scientists who design crumple zones in car frames.
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Even though I’ve worked in the metagenomics / microbiome / microbial genomics space for almost 20yrs…
#SFAF2024
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That time when a (non-
#bioinformatics
) collaborator sends you a multiple sequence alignment of 200 viral genomes...
in an Excel document...
"so I can keep the columns aligned" ...
O M G...
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List of 85+
#metagenomics
pipelines - feel free to reply to this tweet if I've missed anything. Please RT! 😉
#genomics
#bioinformatics
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Finding and Hiring the _right_ people in
#biotech
is hard. There is such a massive shortage of talented, enthusiastic, and sincere people right now - it’s exhausting.
#justsaying
😕😭
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Kindly: please retweet if you see this important notice.
Today at
@officialatcc
, we announced a change to the access model for the ATCC Genome Portal (). In order to maintain its long term sustainability, we are transitioning to a Supporting Membership
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I'm very happy to announce I've received a joint faculty appointment at
@SyracuseU
's Forensic & National Security Sciences Institute (
@SUForensics
)!
What's next?
#STEM
training & research projects in
#genomics
and
#bioinformatics
w/my team at
@officialatcc
@ATCCgenomics
☺🦠🧬🚀
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Bioinformaticians be like “I know a spot” and then they take you to /var/opt/local/bin and tell you everything “just works” here - but they don’t know why.
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Every time I put on these warm DNA socks I remember how important conference swag that lasts is - thanks again
@PhaseGenomics
!
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We just completed our latest release- and this month we surpased 3,500 microbial genome assemblies on the ATCC Genome Portal!!! I'm so stoked! 🏄♂️😊🧬
#genomics
#bioinformatics
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@remax281
@fawfulfan
This is wrong. Please delete your tweet and then go talk to some actual professors in the US before tweeting about how academia works.
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Omg. Cleaning out our basement storage area and I found this box of grad school gold 🌟📚 and
#bioinformatics
history. some of these must be ~20 yrs old…
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We went as a family to Germany over the holidays. It was great. 1st time my kids went to Europe.
Yesterday at the grocery, my son says
Dad, I think Germany “does it better”
Does what?
Shopping bags, Recycling, Trains, Tipping, Museums, city walking areas, fireworks
😂
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Ongoing project in my group is unraveling the methylomes of the ~3000 different bacterial species we have sequenced on
@nanopore
over the last 3 years at ATCC. Hoping to share those results later this year and make the data available via the ATCC Genome Portal.
Traditional
#methylation
detection techniques are limited due to short read lengths, bias, & complex library prep.
In this workflow learn how nanopore sequencing overcomes these challenges to deliver a new gold-standard for methylation calling:
#WYMM
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We’re growing! I’m hiring! Please RT! 😁
Do you NGS?
Are you are a recently minted PhD or PostDoc who gets fired up about
#ASMicrobe
,
#genomics
,
#bioinformatics
,
#microbiome
or
#AMR
?
Curious about Industry?
Multiple positions in Denmark open now 🧬😊🧬
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72% of all biological resource databases disappear.
Thanks
@cthoyt
for this great presentation:
Promoting the longevity of curated scientific resources through open code, open data, and open/public infrastructure (O3)
#bioinformatics
#biocuration
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This required reading. 🤣
#bioinformatics
A cartoon guide to bioinformatics by a novice coder
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Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies |
@ASMicrobiology
@mSphereJ
#Bioinformatics
#genomics
😊🧬🦠🧫
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Ok - after chatting with
@PalantirTech
, I’m pretty excited about potential use of their platform for ontology and data modeling for
#bioinformatics
and
#genomics
.
#GartnerSYM
(cc:
@DrSnOU
)
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Ok - just went out to see the new
@DnDMovie
with about 20 other people - mostly ttrpg gamers and some non gamers in the mix.
Everyone came out laughing and talking about the film. loved it. All around a super fun time.
Highly recommend
#DnDHonorAmongThieves
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Two important
#genomics
updates today. Please ❤️/RT!🙏
1/Today another 400 authenticated reference genomes were released to the ATCC Genome Portal! Bringing us to 4,500🥰 More coming (1000/year) and we plan to sequence the entire collection.
But we can’t do this alone👇
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Here are the # of microbial genomes we've sequenced by genome size
#ICYMI
#virology
#mycology
#bacteria
#microbiology
See the whole collection of
#genomics
data from
@officialATCC
here:
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Love it when I find metadata like this in GenBank... 😐
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Considering we likely have one of the most diverse collections of
@nanopore
+
@illumina
data for microbial genomes (w/standard methods, 2300+ strains, 1000+ diff. species) we can / will confirm this! 👍👍 TY
@MadsAlbertsen85
💪🙏
#genomics
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If you attended
#ASMicrobe
- please do yourself and your community a favor and test yourself for
#COVID19
when you get home. A negative result made me happy but I know a few people who tested positive and bad to head home early.
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WOW... we got over 25 applicants for the biocuration position on my team at ATCC. That's a first. It's incredibly hard to find good people in lifesciences right now, so I'm def.
#feelinggood
! 🥳
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OMG - had an early preview today of our new fully automated
@Nanopore
library prep workflow using our
@Eppendorf_USA
EPMotion 5075. Just awesome work by a couple of talented biologists on my team. Minimal hands on time - 32 libs per run (could be more). Looking to share code soon
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Wow!🤩 The ATCC Genome Portal now has 3,118 authenticated microbial reference genomes!
What's new?
+169 bacteria
+3 fungi
+2 viruses
Likely our biggest monthly update ever!
#genomics
#bioinformatics
#microbiology
#ILoveMyJob
cc:
@officialatcc
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@aetiology
I’ve had 3 people DM me in few days with (paraphrasing) : I don’t follow you for political liberal stuff, just science
One person asked me to stop RTing protestor stuff
I said No
They all unfollowed me. 🙄
I guess we create our own silos
And this country is F’d right now
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So-good news. Today is day 3 of no fever for my son who has been sick the last 12-13 days with COVID19. Tomorrow he can come out of isolation upstairs🎉And bad news: it’s supposed to drop to 33°F tonight. It’s May! WTH?! I planted a garden this year>gods must have been angered 😢
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This is my team
@officialatcc
@ATCCgenomics
. We just finished our annual all hands kickoff meeting. Every one of them rocks.
feels so great to work with such an awesome group of
#genomics
and
#bioinformatics
scientists.
🙌🧬👍🎉🎉
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Massive turnout for
@BSingletons
- I’m so freaking happy for
@JoeTCJ
and
@AmandaLynGunn
- what a huge success
@ASMicrobiology
#ASMicrobe
!!! I mean… think about it… all these ECS went miles away to an offsite location for this. A huge barrier - but they still came. Just
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OMG... this is just hilarious and so
#cringy
...
Rumor has it that the marketing guy who made this was fired. Is that true
@Eppendorf_USA
? If so - that's so sad... bc this is brilliant. 😂
#biotech
#automation
#genomics
#bioinformatics
#boybands
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🚨🧬🦠Great News! Just received approval to provide
@QIAGENBiox
CLC
#Genomics
ProSuite for free to any and all
#publichealth
or clinical microbiology labs who are sequencing or doing
#bioinformatics
of
#SARSCOV2
, the
#coronavirus
that causes
#COVID19
. Read this thread for details
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I'm working on a new google doc cataloging public
#microbiome
/
#metagenomics
data.
Anyone know of a systematic review of all available dbs in this space? Or a public document?
both 16/ITS and shotgun data
And-yes I'll share the doc once ready-and no SRA doesn't have it all 😄
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de novo assembly pipelines are all educated guesses...
If you've ever run multiple assembly pipelines on the same data > do a whole genome alignment of the different assemblies they spit out - you'll see what I mean. Makes me feel...
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