Share this page!

Lior Pachter Profile picture
Twitter logo
28 Jan, 11 tweets, 3 min read
"The new answer to a 77-year-old problem"

😭
You've come this far and you're thinking... oh... but plot the difference...

Ok. biorxiv.org/content/10.110…
Or this. thenode.biologists.com/quantification…
I will say, box plots / dynamite plots are a terrible way to display data and too many people still use them. But people make a lot of poor choices in their figures. Since you've come this far I'll share this ultimate useless figure... enjoy Figure 1... jstor.org/stable/2291148…

• • •

Missing some Tweet in this thread? You can try to force a refresh
　

Keep Current with Lior Pachter

Lior Pachter Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @lpachter

Lior Pachter Profile picture
29 Jan
This past week my lab published 4 @biorxivpreprint papers in applied math (biorxiv.org/content/10.110…), biology (biorxiv.org/content/10.110…), bioinformatics (biorxiv.org/content/10.110…), and instrumentation (biorxiv.org/content/10.110…). They were possible thanks to reproducibility... 1/ ImageImageImageImage
There is a lot of focus on the importance of reproducible science for facilitating replication of published research. That's all good, but reproducible science has another benefit: when adopted by a group it is an incredible accelerant for research *in that group*. 2/ Image
Consider the paper we wrote on whole animal multiplexed #scRNAseq. The @GoogleColab notebooks Tara Chari wrote for the analyses were a monumental effort, but she did not start from scratch. 3/
Read 8 tweets
Lior Pachter Profile picture
29 Jan
Happy to announce a new open-source instrument from our lab, this time a low-cost, scalable, and automated fraction collector for fluidics applications. Beautiful work by @sinabooeshaghi & @annekylosaurus, with @lioscro and @JaseGehring. 1/
biorxiv.org/content/10.110…
The design is simple and elegant. A single motor drives the shaft of the tube rack, which is coupled to the dispenser arm via a spiral track. This ensures both rotate in tandem. 2/ Image
The device is easy to 3D print and build, and can be assembled from off-the-shelf parts in less than an hour for $67.02. This low cost, and the straightforward assembly, is possible thanks to the design around a single motor. Amazing work by @annekylosaurus & @sinabooeshaghi. 3/
Read 12 tweets
Lior Pachter Profile picture
28 Jan
Universal Health Services @UHS_Inc is the largest facility-based behavioral health provider in the country. Its mission statement includes "To provide..healthcare services that..INVESTORS seek for long-term returns."

Hard to believe right?

This is straight from their "mission statement" website, capitalization and all... uhsinc.com/mission-statem…
Last year UHS settled with the DOJ for $122 million. complianceweek.com/regulatory-enf…
Read 5 tweets
Lior Pachter Profile picture
25 Jan
New preprint from our lab on whole animal multiplexed #scRNAseq (WHAM-seq) by Tara Chari, Brady Weissbourd & @JaseGehring et al. collaborating w/ David Anderson, Evelyn Houliston @Clytia_Vlfr, and @richcopley. A 🧵 about our proof of principle in🎐... 1/ biorxiv.org/content/10.110…
We show #scRNAseq can be used for "reverse genomics" to conduct low-cost *experiments*. Instead of sequence first ask questions later, we ask questions first & then sequence. We illustrate the approach w/ a starvation experiment using the emerging model Clytia hemisphaerica. 2/ ImageImage
We performed multiplexed #scRNAseq using the ClickTag approach developed in our lab by @JaseGehring (w/@sisichen, Matt Thomson, Jeff Park). The chemical multiplexing can be used on any tissue/animal and facilitates experiments with little batch effect. 3/ nature.com/articles/s4158…
Read 16 tweets
Lior Pachter Profile picture
8 Dec 20
There are some difficult truths when it comes to publication modes and publication costs, and @rsidd120 makes some good points here.

His on-point thread reminded me of my black and white paper: 🧵
In 2006 I went on a year-long sabbatical to @UniofOxford from @UCBerkeley. My grants were just ending and I thought I'd reset by doing some math after several years of genome consortia (I didn't have a biology mentor to tell me R01s can be renewed, so I didn't know & didn't try).
At @UniofOxford I was hosted by Philip Maini in Maths and @JotunHein in the Stats. It was a fun year in which I met @satijalab who was a student at the time. We ended up writing a paper on phylogenetics, alignment and annotation: academic.oup.com/bioinformatics…
Read 12 tweets
Lior Pachter Profile picture
7 Dec 20
A thread about curated databases in genomics:

The first database I curated by hand was for my Ph.D. thesis. It consisted of a database of 117 orthologous human and mouse genes (this was in the late 90s before either genome was sequenced!). It's still up: cb.csail.mit.edu/cb/crossspecie…
Compiling this database was hard. It required combing through GENBANK, performing alignments to check for orthology, examine proteins for homology etc. The database was generated for benchmarking a gene prediction tool, but I found that the curation had much more value than that.
The process of compiling the database taught me a ton about the state of gene sequences in GENBANK, challenges in sequence alignment, functional annotation etc. I learned a lot making this database. Also others found it useful in derivative work: korflab.ucdavis.edu/~genis/documen….
Read 12 tweets

Did Thread Reader help you today?

Support us! We are indie developers!

This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Too expensive? Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal Become our Patreon

Thank you for your support!

Follow Us on Twitter!

Like this author's thread?

Get emails when @lpachter has new unrolls!

Check out other threads from @lpachter!

Read all threads by @lpachter