Evan Biederstedt

[Sara C Käufler @SaraCSchulte]

Excited to share our paper on somatic variant calling in HLA genes and genes related to antigen presentation across a cohort of 136 patients with diffuse gliomas published in @CIR_AACR: https://t.co/5NWRoGjXva

A thread ...

#Bioinformatics #Immunology #CancerResearch

[allen institute @AllenInstitute]

Did you make a cool #OpenScience tool using Brain Map? Submit it to our community tools page!

Tools should use Brain Map resources, extend the use of data, provide new ways to access and analyze data, or support educational use.

Learn more and submit:
https://t.co/BvJKbMhS1a

[Jonathan Mitchel @J_E_Mitchel]

It's great to see my first paper of the PhD published in @NatureBiotech! https://t.co/uMnJ6Z1g3C. This describes our scRNA-seq method, scITD, for analyzing how the transcriptional states of multiple cell types are linked across patients. A few highlights from the paper:

[Vladimir Seplyarskiy @seplyarskiy]

Finally published. In this paper we showed that despite heterozygous exonuclease deficiency of pold1 has a minor effect on the germline and somatic mutation rate. Homozygous deficiency increase mutation rate by 2 orders of magnitude and causes cancer https://t.co/fFBK2eeMo8

[Holger Heyn @hoheyn]

ENJOY READING:

A Human Tonsil Atlas @ImmunityCP

Proud to present our @humancellatlas work generating an "Atlas of Cells in the Human Tonsil" at #singlecell resolution and 5 modalities.

Thanks @ERC_Research and superstar-teams @cnag_eu and @idibaps.

https://t.co/6Kxt74TUXv

[Teng Gao @tGaoTeng]

Aneuploidy is a defining feature of cancer cells, but is it also present in healthy normal tissues? In our paper out today on @NatureGenet, we report hundreds of mosaic chromosomal alterations (mCAs) found in diverse tissues from #GTEx. A thread (1/7)
https://t.co/JtzP7d1oRL

[Elisabeth Bik @MicrobiomDigest]

@PetukhovViktor Viktor Petukhov @PetukhovViktor talks about his winning paper, 'Cell segmentation in imaging-based spatial transcriptomics', published in
@NatureBiotech
It deals with the problem of false individual-cell signals from neighboring cells. See: https://t.co/jOmhalDMkA
#BC2Basel

[Evan Biederstedt @EBiederstedt]

@shyam_lab For really high impact, coupled ODEs and nonlinear dynamics might do the trick. Say "goodbye" to Manhattan plots, and "hello" to bifurcation diagrams and Mandelbrot sets. :)

[BCM HGSC @BCM_HGSC]

⌛️Time's running out to sign up for our #Bioinformatics #hackathon, Aug 30-Sept 1! Dive deep into SV, somatic & mosaic variants, graph genomes, and more! Prizes for best teams!

Registration closes 3pm CT Friday!
https://t.co/d62ywPB7hj

[Steven Salzberg 💙💛 @StevenSalzberg1]

Major, fatal errors found in the data and methods of a 2020 paper in @Nature, including millions of reads mis-identified as bacteria. The "cancer microbiome" in this study was simply not there. @abrahamgihawi @elapertea @YuchenGe1 @JenniferLu717 https://t.co/z5Aja84kiR

[Evan Biederstedt @EBiederstedt]

@shyam_lab @nicholas_navin @hoffman_steven @ItaiYanai @TiroshLab @KeystoneSymp +1
It's probably the coverage required which is what makes this so costly. The low VAFs are needed for virtually everything (tracking clonality, LOH detection for SCNA callers, etc.)

[Evan Biederstedt @EBiederstedt]

@shyam_lab @nicholas_navin @hoffman_steven @ItaiYanai @TiroshLab @KeystoneSymp I still think you'd need matched genome sequencing at a significant depth (A) to confidently call variants and (B) capture all the heterogeneity at play. Why? Even long-read scRNAseq is sparse and still the error-rate is too high, especially for somatic variants.

[Fritz Sedlazeck @sedlazeck]

Really excited that @naturemethods highlights our method Read2Tree. Nice writeup on why @DessimozLab (@ddylus @SinaMajidian) & we (@BCM_HGSC) are so excited about it!

@ddylus @SinaMajidian @AdrianAltenhoff #Bioinformatics
Git: https://t.co/w2Hxr7YS3n
https://t.co/STTzI4tdhU

[Ewan Birney @ewanbirney]

It was a tour de force just generating a draft human pan-genome @HumanPangenome, but some suspected and some utterly bizarre things about the human genome have been revealed using these 47 different human reference quality genomes.

[Pesho Ivanov 🇺🇦 @peshotrie]

Alignment types viz 2.0 by @curious_coding and me. thanks for suggestions @pashadag, @chirgjain and @krsahlin!

[Evan Biederstedt @EBiederstedt]

@shyam_lab I think it will significantly correct our understanding as well :) Short-read SV callers notoriously suffer from FP calls...

[Jason Chin @infoecho]

Great thing to learn from experts: Variant calling and benchmarking in an era of complete human genome sequences

Congratulations! @GenomeInABottle @sedlazeck

https://t.co/SrKa9C3mwf

[Yida Zhang @YidaZhang0628]

Need to design gene panels for targeted spatial transcriptomics technologies? Read our new pre-print “Gene panel selection for targeted spatial transcriptomics” https://t.co/dwVbbVjgqm. In this work, we developed a computational method, gpsFISH, to perform such gene panel design.

[Evan Biederstedt @EBiederstedt]

@notSoJunkDNA Your audience is confused!
https://t.co/yn4ew8Xsdp

[Nicolas Robine @notSoJunkDNA]

Starting now, I will only tweet about preprints 1/n

[Evan Biederstedt @EBiederstedt]

@satijalab [lazy request] I wish you would create an "Add to calendar" link. :) Google Calendar, etc.