Pall Melsted @pmelsted Twitter profile

Last Seen Profiles

@wamuusama

@Rmy__5

@StateOfDecay

@Jimmy_Fremgen

@LucasLechero

@minahrly

@kold_1st

@vip_Trika

@ChiefBiddle_r

@Derpeeh

@DaysSword

@wtf_max18

@jasminsissy2008

@stw_pdg

@ParkermusicSV

@KGirl586

@ltrlymnylr15651

@zrafy

@dani___gp

@PBHammond

@Buy_Simu

@alfredocejar

@jyou10

@GeauxSeeTheLady

@bokeplokalmalam

@DeepWorlds_SA

@umithan35

@CreekstoneFarms

@klmnight

@yaho_ns

@qasslaw

@Ugo_001

@RosetaPauly

@shyAway_Games

@P3VFyi2OrmCAH6k

@ogoevnurik

Pall Melsted

@pmelsted

6 months

In this preprint with @sindri_e we compared seven widely used methods for batch correction of single cell RNA-seq data. We found that all but one of the methods introduce batch effects when there are none. 1/N

Batch correction methods used in single cell RNA-sequencing analyses are often poorly calibrated

As the number of experiments that employ single-cell RNA-sequencing (scRNA-seq) grows it opens up the possibility of combining results across experiments or processing cells from the same experiment...

www.biorxiv.org

5

138

474

Pall Melsted

@pmelsted

6 years

I'm pretty sure my morning coffee changes my gene expression by more than 7%

5

88

483

Pall Melsted

@pmelsted

4 years

Exactly one month ago Iceland had 1045 active diagnosed infections. Today we have 99 active, and added 608 new cases during this time, most of which have recovered. #TestTraceIsolate

5

59

214

Pall Melsted

@pmelsted

6 years

Today I am doing proper bioinformatics. Matching up gene symbols between databases

11

15

207

Pall Melsted

@pmelsted

4 years

A twitter play with three acts

2

34

201

Pall Melsted

@pmelsted

6 years

Next time your kid loses a tooth, put it in a coke-bath and have them watch what happens. There is an important lesson to be learned 1/n

2

57

142

Pall Melsted

@pmelsted

7 years

New release of kallisto is out kallisto can now produce BAM files in genomic coordinates, sorted and indexed for IGV consumption, details in a new blogpost Oh, and it runs on a tiny computer

Bioinformatics on a Rock64

I have been fascinated with mini computers for some time, and have wondered when they will become suitable for bioinformatics. The 4273π project, which is an online course that is distributed as a …

liorpachter.wordpress.com

3

85

136

Pall Melsted

@pmelsted

6 years

Society will teach your kids about dental hygiene, dangers of soda drinks, but who is going to talk to them about experimental design? 4/4

4

19

132

Pall Melsted

@pmelsted

4 years

Speed is crucial in fighting this epidemic. In Iceland we use test-trace-isolate to curb the spread in addition to restrictions on social gathering, 2m social distancing and mask wearing in public. Here is a rough timeline of what happens for a positive diagnosis

3

43

125

Pall Melsted

@pmelsted

5 years

I can solve every problem with a combination of cut,grep,sed,sort,uniq, and awk

5

13

123

Pall Melsted

@pmelsted

7 years

Transcripts are real, genes are a useful abstraction #gi2017

4

45

114

Pall Melsted

@pmelsted

7 years

I am a real bioinformagician, I can do analysis stuff without first converting data into tabular form

8

16

111

Pall Melsted

@pmelsted

6 years

New preprint out w @lpachter & @vntranos on the Barcode, UMI, Set format (BUS) for processing of single cell RNA-Seq datasets. Shows how to create modular frameworks for processing scRNA-Seq data, fast using kallisto (v 0.45.0 just released) and simple

2

46

109

Pall Melsted

@pmelsted

3 years

Recursive vaccinations! My brother got his first and only J&J/Jansen shot today. Yes, that’s a tattoo of himself

2

11

102

Pall Melsted

@pmelsted

4 years

deCODE genetics is has stepped up to assist with covid19 screening in Iceland. Started last Friday and have completed 1800 tests and are operating at a rate of 1000 tests per day. That’s 0.3% of the population per day.

Íslensk erfðagreining

19 jákvæð sýni af 1800 Búið er að taka 3087 sýni í Þjónustumiðstöð rannsóknaverkefna í Turninum í Kópavogi. Þegar greind hafa verið 1800 sýni hafa fundist 19 jákvæð. Enn bendir því allt til þess að...

www.facebook.com

3

32

98

Pall Melsted

@pmelsted

4 years

Border screening in Iceland has detected 13 cases of the British variant. Twelve came from the UK, one from Denmark. Every positive sample is sequenced.

0

20

93

Pall Melsted

@pmelsted

6 years

Break it to them gently that their paper got rejected because reviewer 3 had serious concerns about lack of negative control 3/4

2

10

93

Pall Melsted

@pmelsted

6 years

Gene databases: so there is this gene called LAMP3 Me: sounds good Gene db: but wait there is also CD63 Me: ok? Gene db: and it’s also known as LAMP-3, I mean what could go wrong Me: [...]

11

19

89

Pall Melsted

@pmelsted

8 years

Good news: I have tenure. Bad news: I'm the new department head.

12

8

89

Pall Melsted

@pmelsted

3 years

Iceland has found 12 cases of omicron confirmed with sequencing. All PCR positive cases are sequenced. Since the first report of omicron, all S dropouts have been sequenced within 24 hours. The US has confirmed 20 cases, how large is the the iceberg?

7

15

86

Pall Melsted

@pmelsted

5 years

Yesterday was my 10 year anniversary in bioinformatics. Thanks to @jkpritch for taking a chance on me when I knew nothing about genomics, sequencing, and rna. Heading out to #ASHG19 now

1

2

86

Pall Melsted

@pmelsted

6 months

The paper is the result of this thread pulling. My advice is twofold and simple. 1. just use Harmony 2. if you are correcting for batch effects, make sure it does nothing when there are no batch effects. 9/N (N=9)

3

10

87

Pall Melsted

@pmelsted

4 years

Every polynomial has their day

Jordan Ellenberg

@JSEllenberg

4 years

Well, I'll be damned, it really is a cubic.

200

3K

15K

1

8

84

Pall Melsted

@pmelsted

3 years

Triple blind review. Authors don’t know the identity of reviewers and vice versa. Reviewers don’t know the identity of the journal. Should the quality of review and rigor depend on where it was submitted?

8

4

75

Pall Melsted

@pmelsted

4 years

The paper from @decodegenetics on the spread of SARS-CoV-2 in the Icelandic population is finally out proud to have worked on this with @hakon_jon and others

3

32

74

Pall Melsted

@pmelsted

8 years

. @NatureNews you know the image is of JavaScript code, right?

1

15

71

Pall Melsted

@pmelsted

5 years

Bifrost – Highly parallel construction and indexing of colored and compacted de Bruijn graphs. Paper by @GuillaumOleSan and myself, constructs colored de Bruijn graphs for 118K Salmonella strains. Software: , preprint:

Bifrost – Highly parallel construction and indexing of colored and compacted de Bruijn graphs

Motivation De Bruijn graphs are the core data structure for a wide range of assemblers and genome analysis software processing High Throughput Sequencing datasets. For population genomic analysis,...

www.biorxiv.org

1

24

70

Pall Melsted

@pmelsted

9 years

uniq on mac only compares first 8kb of line, use sort -u instead #waytoospecificcmdlineadvice

12

59

68

Pall Melsted

@pmelsted

3 years

I’m psyched about the vaccine lottery this week in Iceland. No $1M prize, we will randomly draw a birth year (1975-2005) and all born on that year will be vaccinated that time. And we’ll keep going till we’re done. 🤞1980

3

4

65

Pall Melsted

@pmelsted

4 years

Since we are cleaning up gene names for excel, how about we don’t put a slash in the name. Pretty please

3

6

62

Pall Melsted

@pmelsted

8 years

Kallisto is published. I've had some straight-to-video papers, this is not one of them

4

62

59

Pall Melsted

@pmelsted

6 years

My phone has learned how to spell ensembl, pseudoalignment and Rnaseq. Ducking amazing #DeepLearning

4

3

58

Pall Melsted

@pmelsted

2 years

Genome informatics 2022 will be held as a hybrid conference in Hinxton, UK Sep 21-23 this year. Right now you have one week to submit your abstract for #GI2022 (deadline July 12th) You know what to do.

Genome Informatics — 20220921

Methods for analysis of large genomic data sets

coursesandconferences.wellcomeconnectingscience.org

1

20

55

Pall Melsted

@pmelsted

6 years

We have a position available at the University of Iceland building up bioinformatics services as well as working on bioinformatics in my group. deadline is april 18th, plz retweet.

7

109

52

Pall Melsted

@pmelsted

4 years

Yesterday Iceland received 10K doses of the Pfizer vaccine (for 5K people). Today 2.5K were vaccinated and we will finish the doses tomorrow. Throughput is estimated to be at least 10K per day. Scaled up to the US this corresponds to 2.5M people.

3

10

52

Pall Melsted

@pmelsted

3 years

New preprint out, lead by @kreldjarn & @SolviStats Two key results. 1. Reconstruction of a giant infection tree with 2500+ infected individuals from the "third wave" of covid in Iceland. 2. Using this tree to simulate the effect of vaccinations 1/5

Reconstruction of a large-scale outbreak of SARS-CoV-2 infection in Iceland informs vaccination...

The spread of SARS-CoV-2 is dependent on several factors, both biological and behavioral. The effectiveness of various non-pharmaceutical interventions can largely be attributed to changes in human...

www.medrxiv.org

1

18

52

Pall Melsted

@pmelsted

9 months

Genome Informatics 2023 is about to start #gi2023

2

5

50

Pall Melsted

@pmelsted

9 years

I don't always analyze RNA-Seq in the cloud. But when I do, I'm at 30k ft on my laptop http://t.co/wImr7XBalJ #bog15 http://t.co/BLQtBBedkh

3

18

48

Pall Melsted

@pmelsted

9 years

If you are struggling with understanding BWT on graphs, look at interactive viz from my student @Moyaccercchi

3

33

51

Pall Melsted

@pmelsted

3 years

I’ve written software that eats millions of reads in a matter of 10 seconds. I don’t hesitate grepping huge files and feeding them into a series of pipes of awk/cut/sort/uniq that I write with my eyes closed. But canvas takes 10 seconds to list discussion items 🤷

2

1

50

Pall Melsted

@pmelsted

6 years

Hate is a strong word, but I really hate GTF files

5

7

47

Pall Melsted

@pmelsted

5 years

My brains feels like mush. It’s either because I’m 40 today or the 8 hour jet lag, can’t tell because batch effects

5

0

49

Pall Melsted

@pmelsted

6 years

Setting up new computer: 0 min, where did all the brew packages go? 2 min, what is this bioconda thing I keep hearing of 5 min, why didn't anybody tell me about this thing before ?!?

6

7

45

Pall Melsted

@pmelsted

8 years

5yo daughter: "we really only have 4 fingers, see 0,1,2,3,4" #soproud #csparenting

2

16

44

Pall Melsted

@pmelsted

8 years

Whoever decided to name the yeast chromosomes I-XVI rather than 1-16 was not a fan of shell scripts

3

26

43

Pall Melsted

@pmelsted

8 years

Next time I give a talk in England this will be my title slide

2

8

43

Pall Melsted

@pmelsted

8 years

Don't get me wrong, I love R, some of my best friends use R, but it's the javascript of data science (not a complement)

2

27

40

Pall Melsted

@pmelsted

4 years

@mbeisen If you are using R for data analysis just drink the tidyverse koolaid. This is a very helpful book and how I got up to speed using it

1

2

39

Pall Melsted

@pmelsted

1 year

Suffix tree / k-mer / FM-index

1

3

37

Pall Melsted

@pmelsted

7 years

tail -n+2 removes the first line from the input #whywasntItaughtthis

7

6

37

Pall Melsted

@pmelsted

5 years

Thesis defense starting for @hannespetur my first PhD student, joint with @bvhalldorsson

1

3

37

Pall Melsted

@pmelsted

7 years

There is p-value hacking and then there is p-value hammering

1

7

37

Pall Melsted

@pmelsted

1 year

22 years of studying sorting algorithms finally paid off

3

2

36

Pall Melsted

@pmelsted

4 years

I just had a covid test as a random sample from the population. I timed the visit, 4 minutes and 50 seconds from entering the building until walking out again. Results are promised within 24 hours, but I’m guessing I’ll know later tonight.

2

5

34

Pall Melsted

@pmelsted

1 year

gzip is the new logistic regression

2

34

Pall Melsted

@pmelsted

4 years

The data behind this figure is based on contact tracing for about 1200 individuals. Each trace requires about 20-200 phone calls and is done by a dedicated team at @almannavarnir working hard to contain the spread

Antonio Regalado

@antonioregalado

4 years

The report from DeCode and Kari Stefansson is out. "Spread of SARS-CoV-2 in the Icelandic Population" They tested 6 % of Iceland population. Found 0.6-0.8% infected. Charts show transition from imported case to family spread in a month.

4

62

80

0

8

33

Pall Melsted

@pmelsted

7 years

It's not just that I hate the GTF format, I hate that nobody can agree exactly on how to use it #ivegot99bioinfoproblemsandGTFisallofthem

2

6

33

Pall Melsted

@pmelsted

3 years

A member of parliament in Iceland(stepping in as a substitute for another MP who is infected with Covid) is trying to get an isolation of Covid positive individuals thrown out in the courts. Ironically, not for the MP he is substituting for. 1/4

2

6

33

Pall Melsted

@pmelsted

8 years

Thoughts on NP-completeness and Bioinformatics related to thread cc: @spadesassembler @pierre350d @NPMalfoy

Does NP-completeness have a role to play in Bioinformatics?

tl;dr: yes Earlier this year I attempted to review a paper that had an NP-completeness result for aligning reads to de Bruijn Graphs. I say attempted, because I received an invitation to review the…

pmelsted.wordpress.com

1

29

32

Pall Melsted

@pmelsted

5 years

If you’re feeling extra charitable you can stop calling them a geek

Rafael Irizarry

@rafalab

5 years

Dear everybody, If you have to choose one nice thing to do for the computer geek helping you, don't use spaces in your filenames. Instead of "My Document", use "my-document", "my_document" or "myDocument" Spaces indicate the end of the filename in some of the tools we use.

17

196

736

3

6

32

Pall Melsted

@pmelsted

3 years

0.4% of all Icelanders were diagnosed PCR positive for Covid yesterday. Scaled to the US that’s like 1.5M in one day. Elementary schools will open Jan 4th and 5-11y vaccinations will begin on Jan 10th. What could possibly go wrong.

3

31

Pall Melsted

@pmelsted

1 year

@iddux Bioinformatics algorithms by Pevzner and Compeau. The alignment chapter alone is worth it because it emphasizes understanding over implementation details. Rosalind problems are a fantastic addition to just studying the text

4

6

31

Pall Melsted

@pmelsted

4 years

Contact tracing has significantly reduced the spread of the virus. But it’s not enough by itself. Do your part. Limit social interactions, wear a mask, get tested ASAP for symptoms /end

3

2

32

Pall Melsted

@pmelsted

7 years

If you feel like there is an impeding doom where deep learning will eat your data analysis lunch, just watch this

Barbara Engelhardt

@BeEngelhardt

7 years

My TEDx talk on the importance of building interpretable, open box machine learning models and using domain-informed detective work to accelerate discovery in genomics, biology, and medicine:

6

188

511

1

6

31

Pall Melsted

@pmelsted

6 months

We argue that it is better to not modify the cell-by-gene matrix at all but rather to correct objects which affect clustering. Downstream statistical tests can then take the batch identifier as a covariate, e.g. linear models or MAST. 6/N

1

3

31

Pall Melsted

@pmelsted

9 years

Introducing the Bioinformatics Ironman: write an assembler, a short/long read aligner and a file format

3

17

30

Pall Melsted

@pmelsted

4 years

Very interesting analysis of the choices made when designing the Biontech/Pfizer mRNA vaccine. So much of this builds on top of decades of basic scientific research. Our public research funds hard at work.

0

9

29

Pall Melsted

@pmelsted

3 years

Omicron’s fake move of (maybe) appearing to be a milder disease while spreading faster is an ankle-breaker and politicians seem to be falling for it.

1

7

29

Pall Melsted

@pmelsted

7 years

Bioinformatics pro tip: keep an unpatched system to benchmark your programs and a patched one for anybody else's

2

12

27

Pall Melsted

@pmelsted

6 years

After one week examine the tooth and discuss what happened and the likely causes. Ask them to write up a short report 2/n

1

6

28

Pall Melsted

@pmelsted

7 years

Graphtyper paper is out congrats to my phd student @hannespetur and co: @bvhalldorsson @hakon_jon @BirteKehr

1

15

27

Pall Melsted

@pmelsted

2 years

Open up Rstudio library(writexl) ?write_xlsx wait for it ...

2

5

28

Pall Melsted

@pmelsted

2 years

Great start for Genome Informatics 2022, first in-person meeting since 2019, with @ceclindgren giving the first keynote #gi2022

0

3

27

Pall Melsted

@pmelsted

3 years

Vaccinated

1

0

26

Pall Melsted

@pmelsted

7 years

Graphtyper, first paper/preprint by my phd student @hannespetur is out @bvhalldorsson @decodegenetics

0

27

Pall Melsted

@pmelsted

9 months

That's a wrap for a great Genome Informatics conference #gi2023 See you next year in Hinxton, UK btw, the cover had a small easter egg, let me know if you can find it

1

4

26

Pall Melsted

@pmelsted

10 years

. @jaredtsimpson @assemblathon exhibit A http://t.co/MdKqG87vVO

4

29

27

Pall Melsted

@pmelsted

6 years

. @ggonnella talking about GFA format , grew out of a blog post …, @lh3lh3 proposed GFA in another blog post …, specification came later and improved to GFA2 which generalized better for long read technologies #GI2018

Dear assemblers, we need to talk … together

This post was co-authored by Michael R. Crusoe @biocrusoe and thanks to Shaun Jackman @sjackman for discussions and reading the draft. tl;dr we need a common file format for contig graphs and other…

pmelsted.wordpress.com

1

15

25

Pall Melsted

@pmelsted

4 years

Important life lesson: geologist use the concept “it will happen in the next hours or so” much like bioinformaticians

1

5

27

Pall Melsted

@pmelsted

6 years

De Bruijn graphs with even k are just fine, also it doesn’t matter how you pronounce de Bruijn

0

2

27

Pall Melsted

@pmelsted

3 years

Mix-n-match second dose today: Jansen + Moderna, 7 weeks apart. Will report on side effects (n=1)

2

0

27

Pall Melsted

@pmelsted

3 years

0

2

25

Pall Melsted

@pmelsted

5 years

8yo daughter: Hey Siri can you do my homework? Siri: in the words of Aristotle “the roots of education are bitter, but the fruit is sweet”

0

5

27

Pall Melsted

@pmelsted

9 months

View from the balcony

2

3

26

Pall Melsted

@pmelsted

9 years

I'm surprised it took me this long to figure out what you call it when you use someone's data: Paracitation #researchparasites

1

23

26

Pall Melsted

@pmelsted

6 years

I’m excited about this and will be until my first poster segfaults

Natalie Telis

@NatalieTelis

6 years

This is really awesome! Next step is to just display a Shiny app where people can play with the data, and really interact with the story - not frozen figure images. The future looks cool 😎📊📈

2

19

0

1

26

Pall Melsted

@pmelsted

2 years

These UMAP jokes have gone too far

0

4

25

Pall Melsted

@pmelsted

3 years

I'll give a short talk on the value of sequencing all SARS-CoV-2 samples in Iceland as part of the #COVID19Nordic research response workshop This Thurs with free reg Great talks from all the Nordics detailing strategies for dealing with the epidemic

1

5

26

Pall Melsted

@pmelsted

4 years

@lpachter This is an improvement, the previous version had a fifth degree polynomial

1

24

Pall Melsted

@pmelsted

4 years

Polar stratospheric clouds

0

4

25

Pall Melsted

@pmelsted

7 years

Fasta has no spec so it's just cool if I use :Þ as a field separator in the name, right?

4

3

25

Pall Melsted

@pmelsted

9 years

BamHash, like md5sum but for comparing FASTQ to BAM: http://t.co/6GCAAnwsAo

2

24

25

Pall Melsted

@pmelsted

3 years

@michaelhoffman @bldgblog @metricausa @ianholmes The review for this paper should have been one of these bicycle memes

0

1

24

Pall Melsted

@pmelsted

3 years

Two volcanoes, one dormant for 1800 years and the other ongoing, visible from our balcony

0

2

24

Pall Melsted

@pmelsted

9 years

High Speed Hashing for Integers and Strings http://t.co/qhkqa9Q2Rx by Mikkel Thorup. Well worth reading for hashing afficionados

4

17

22

Pall Melsted

@pmelsted

7 years

This happened one year ago today and yes I followed through on this

Pall Melsted

@pmelsted

8 years

Next time I give a talk in England this will be my title slide

2

8

43

0

1

23

Pall Melsted

@pmelsted

4 years

That’s some serious math. Your move Stanford

2

1

22

Pall Melsted

@pmelsted

4 years

Yes we’re an island. Yes we are tiny. Reykjavík is not as dense as New York (but similar to urban US cities, eg Pittsburgh). Is it harder to scale this up? Yes, but totally worth it even if it is not 100% effective. #TestTraceIsolate + quarantine close contacts.

1

23

Pall Melsted

@pmelsted

3 years

I got my 3rd dose of vaccine (j&j, Moderna 100, Moderna 50) this morning. I can feel the aches starting up so now is a good time to grade that final exam.

1

0

23

Pall Melsted

@pmelsted

7 years

Listening to the sweet sound of fireworks after Iceland qualified for the World Cup

1

0

23