Liz Tseng @Magdoll Twitter profile

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Liz Tseng

@Magdoll

5 months

If you're studying #bioinformatics , there comes a time when you have to decide between: - staying in academia - going into industry - give up #bioinformtics and do something else Well, let me tell you what it was like for me to work as a #bioinformatics in the biotech

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Liz Tseng

@Magdoll

4 years

You don't see what you don't see if you don't sequence more than 1 genome. Pan-genome of 26 soy bean lines reveal SVs, gene fusions, core/disposable genes. @PacBio

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Liz Tseng

@Magdoll

3 years

#Bioinformatics troubleshooting tip of the day: when it doubt, look at the sequence by eye. Not the alignment, the GFF, or the IGV screenshot. *THE ACTUAL SEQUENCES*. Here's how (using @PacBio Iso-Seq CCS BAM) files as an example: /1

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Liz Tseng

@Magdoll

4 months

A nice review of long-read genome assemblers and its associated #bioinformatics terms

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Liz Tseng

@Magdoll

1 year

As a bioinformatician I am dying at this. Looks like Hollywood should hire me for consulting next time 🤦‍♀️

Oded Rechavi

@OdedRechavi

1 year

When the lab's bioinformatician quits and goes to work for Facebook

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Liz Tseng

@Magdoll

6 years

#ASHG18 is great, but you know what’s better? They have childcare on site, so I don’t have to think about childcare logistics while I’m here. #WomenInSTEM

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Liz Tseng

@Magdoll

3 months

Nice in-depth review of the new T2T / pangenome era by @mike_schatz et al: why gapless human genomes that now have resolved centromeres, telomeres, and segmental duplications and having pangenome to capture genetic diversity is essential to human health.

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Liz Tseng

@Magdoll

2 years

We at @PacBio are finally presenting to the world, at long last, isoform information at #singlecell resolution - some details on the tech background for the kit and #Bioinformatics below 🧵

PacBio

@PacBio

2 years

We’ve partnered with the @broadinstitute and @10xgenomics to launch the Multiplexed Arrays Sequencing (MAS-Seq) kit, an accurate and cost-effective long-read single cell #RNASeq solution. Learn more here: #PacBio #ASHG22

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Liz Tseng

@Magdoll

2 years

#bioinformatics tip of the day: FOLLOW THE DATA. Trace a read through its journey. Example is when I look at a fresh @PacBio Iso-Seq run (but really for any sequencing data for any application). I start w CCS reads, scroll through them to viz the primers and polyA tail. /1

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Liz Tseng

@Magdoll

4 months

Possibly the most complex genome ever assembled of the most harvested (by tonnage) crop in the world - the polyploid sugarcane R570 hybrid - assembled to 8.7 Gb with 12 chromosomes. @PacBio + short reads used for both WGS and RNA-Seq.

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Liz Tseng

@Magdoll

2 years

We showed you @PacBio MAS-Seq #singlecell data on Sequel II/IIe systems, well, now, here it is --- on Revio! Two cells of PBMC data have been released, 110m and 114m reads each.

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Liz Tseng

@Magdoll

2 years

If you like @PacBio Iso-Seq and you like R ggplots2, this is the package for you! ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2 #Bioinformatics #ggplot2 #R

ggtranscript: an R package for the visualization and interpretation of transcript isoforms using...

Motivation The advent of long-read sequencing technologies has increased demand for the visualisation and interpretation of transcripts. However, tools that perform such visualizations remain...

www.biorxiv.org

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Liz Tseng

@Magdoll

4 years

@CA_AstroComm PhD in Computer Science here working in genomics/bioinformatics!

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Liz Tseng

@Magdoll

2 years

The 80s @PacBio vibe continues!

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Liz Tseng

@Magdoll

3 years

Personal #bioinformatics tips that helped me: (1) organize work by year/[author-project]/[month-sample-platform], (2) keep a README for data source, copy email, (3) keep a cmd file (I name it ) in each data analysis folder, (4) keep slides there too

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Liz Tseng

@Magdoll

2 years

Finally read in detail the breast cancer @PacBio Iso-Seq paper and it’s amazing finding - novel isoforms seen only in clinical tumor samples that correlate w survival outcome and cancer subtypes!

A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer

Breast cancer long-read transcriptome profiling reveals patient-enriched isoforms, with implications for disease progression.

www.science.org

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Liz Tseng

@Magdoll

4 years

Plant pan-genomes are the new trend! This is now possible becuz of reduced seq cost, long reads, better algorithms, and the need to understand within-species diversity. A quick thread 1/4 All pub find courtesy of @phototrophic

Plant pan-genomes are the new reference

Nature Plants - This Review summarizes the growth of plant pan-genome studies, explore the origins of gene presence and absence variation, and introduces the impacts of pan-genomes on plant...

www.nature.com

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Liz Tseng

@Magdoll

2 months

Analysis of 170 @PacBio HiFi genomes identified 7000+ segmentation duplications (SD) that comprise 6.1% of the (T2T CHM13) genome. African genomes show higher copy number of multi-copy SDs. Comparing to Iso-Seq data finds 201 novel protein-coding gene in multicopy SDs.

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Liz Tseng

@Magdoll

5 months

LongSom: a #bioinformatics workflow for detecting de novo SNVs, CNAs, #cancer gene fusions to reconstruct tumor clonal heterogeneity. Shows that with @PacBio long-read single-cell RNA-Seq you can reconstruct clones and find clinically relevant SNVs in each clone. Nice work

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Liz Tseng

@Magdoll

3 years

just did bamtools-awk-grep-uniq one liner. I feel dirty and cool at the same time. #Bioinformatics

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Liz Tseng

@Magdoll

1 year

As a preview to the upcoming MAS-Seq for bulk Iso-Seq, here's a @PacBio HG002 MAS bulk x Revio dataset for you to play with! 38 million full-length HiFi reads on 1 Revio SMRT Cell! Enjoy :) More to come.

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Liz Tseng

@Magdoll

2 years

Needless to say I’m all in for @PacBio pink

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Liz Tseng

@Magdoll

3 years

Check this cool baby I'm working on! Single-cell Iso-Seq reads separated by cell types *and* colored by alleles (based on phasing info I ran w IsoPhase). Each alignment is an individual founder molecule. @PacBio #bioinformatics

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Liz Tseng

@Magdoll

1 month

Analysis of ENCODE @PacBio Iso-Seq data using isoLASER (variant calling + phasing + linkage analysis) distinguishes cis- v trans-directed alternative splicing. Finds genetic linkage of splicing is largely individual-specific and enriched in immune genes (e.g. HLA).

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Liz Tseng

@Magdoll

5 years

My @Medium interview w @sedlazeck @MedhatHelmy7 is out! We cover SV calling w long reads, the life cycle of #Bioinformatics tools, why it never hurts to ask for a postdoc you feel unqualified for, and the future for population SV calling!

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Liz Tseng

@Magdoll

4 years

In the coming weeks, I will be releasing a mini series on my @medium blog featuring different @PacBio HiFi assemblers! The interview with @lh3lh3 @ChengChhy (HiFiAsm) has been done and draft is underway. Stay tuned 🥰

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Liz Tseng

@Magdoll

3 months

The news has come out that my company, PacBio, has just gone through a significant layoff. A few notes on this: This says nothing about the high talent of those who were let go. Many of them have contributed critically over the years - some, even before we even had the first

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Liz Tseng

@Magdoll

3 years

Cautionary tale in #BioInformatics : when the results don't look right, and you change the tool parameter (ex: score/length/filter cutoff), and things look *better*, you should NOT think you've saved the day. Most likely, the fault is in the data, not the tool /1

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Liz Tseng

@Magdoll

3 years

Jonas showing the @PacBio HiFi accuracy. Really this is all the amazing work at lots of ppl (me not included) for making this possible. 👏 #AGBT21

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Liz Tseng

@Magdoll

2 years

1/ End of an era for my #bioinformatics contribution to @PacBio Iso-Seq ( #RNA analysis) --- with the release of isoseq3 v3.8.0, I've removed large chunks of now out-dated modules in Cupcake and will be deprecating the rest soon 🧵

GitHub - Magdoll/cDNA_Cupcake: Miscellaneous collection of Python and R scripts for processing...

Miscellaneous collection of Python and R scripts for processing Iso-Seq data - Magdoll/cDNA_Cupcake

github.com

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Liz Tseng

@Magdoll

3 years

. @aphillippy : new complete human genome CHM13v1.1 assembly using PacBio HiFi + ONT UL, no gaps, ~Q70, structurally correct. sees high seq similarity between the acrocentric arms, ~66Mbp new seqs, 1561 new genes. #gi2021

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Liz Tseng

@Magdoll

3 years

Using @PacBio finds long (up to 23kb!) cell-free DNA in maternal plasma with methylation patterns that distinguish tissue origin. potential for NIPT and pregnancy-related risks (ex: preeclampsia)

Single-molecule sequencing reveals a large population of long cell-free DNA molecules in maternal...

In the field of circulating cell-free DNA, most of the studies have focused on short DNA molecules (e.g., <500 bp). The existence of long cell-free...

www.pnas.org

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Liz Tseng

@Magdoll

5 years

Highlighting (what I think are) important bioinformatics tools for long read RNA-seq analysis works by me & @GenomeRIK @anaconesa @DNAwyman @XLR @PacBio #PBUGM

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Liz Tseng

@Magdoll

2 years

The line for the @PacBio #ASHG22 party! #ASHG2022

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Liz Tseng

@Magdoll

26 days

Eichler: PAV, discovery of structural variants by comparing phased (or unphased) genomes against each other. breakpoint resolution. #Bioinformatics #ISMB2024

GitHub - EichlerLab/pav: Phased assembly variant caller

Phased assembly variant caller. Contribute to EichlerLab/pav development by creating an account on GitHub.

github.com

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Liz Tseng

@Magdoll

4 years

One year after tackling its genome, we're releasing the @PacBio redwood Iso-Seq dataset - and here's the @medium blog to go with it! I'll talk about it at PAGday Iso-Seq workshop on Tue too!

Decoding A Coastal Giant: Full-Length Transcriptome of Sequoia sempervirens

Ancient Giants of The Land

medium.com

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Liz Tseng

@Magdoll

1 year

1/ Very excited that this @GenomeBiology paper by de Souza (ETH, Robinson lab) together w @GSheynkman (and me as a honorary middle author XD) on benchmarking DeepVariant/Clair3/GATK/NanoCaller for calling @PacBio Iso-Seq variant data is out!! 🧵

Transformation of alignment files improves performance of variant callers for long-read RNA...

Long-read RNA sequencing (lrRNA-seq) produces detailed information about full-length transcripts, including novel and sample-specific isoforms. Furthermore, there is an opportunity to call variants...

genomebiology.biomedcentral.com

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Liz Tseng

@Magdoll

11 months

First @PacBio MAS-Seq for bulk RNA (Iso-Seq) preprint! Captured full length 7kb RBFOX2 isoforms in Cas13d-mediated knock down

Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox

Alternative splicing is an essential mechanism for diversifying proteins, in which mature RNA isoforms produce proteins with potentially distinct functions. Two major challenges in characterizing the...

www.biorxiv.org

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Liz Tseng

@Magdoll

2 years

Your cheat sheet of @PacBio bulk Iso-Seq publications from the last few months (single-cell Iso-Seq will be in a diff thread), here we go! /1

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Liz Tseng

@Magdoll

2 months

Analysis of @GenomeInABottle and @1000genomes genomes reveal ribosomal RNA diversity not previously discovered - most short indels and GC-rich! Also changes in rRNA variant expression in cancer suggest cancer-specific ribosomes. @PacBio

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Liz Tseng

@Magdoll

4 years

Cool preprint using @PacBio Iso-Seq + RNA-Seq on combined 22 breast cancer samples to find differentially expressed genes *and* isoforms. They were able to define "common" v subtype-specific isoforms. Found five 3-hop fusion genes confirmed w WGS.

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Liz Tseng

@Magdoll

4 years

Diploid potato assembled w 10X+ONT+ @PacBio HiFi+Hi-C, I think I will call this the "kitchen sink potato genome" :P

Haplotype-resolved genome analyses of a heterozygous diploid potato

Nature Genetics - Haplotype-resolved assembly of a heterozygous diploid potato, RH89-039-16, and identification of deleterious mutations provide insights into the genome organization and breeding...

www.nature.com

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Liz Tseng

@Magdoll

4 months

Use of Tomahto, a new targeted mass spec method, combined with @PacBio Kinnex full-length RNA data to to increase detection of isoforms that are turned into proteins - the first step into a personalized proteome. Great work from @GSheynkman lab!

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Liz Tseng

@Magdoll

4 years

The latest @PacBio Iso-Seq #Bioinformatics software landscape. Want to know more about it? Come to the Global Summit next week!

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Liz Tseng

@Magdoll

6 months

Spatial transcriptomics at isoform resolution reveals isoform switching events in heart tissue post myocardial infarction - here's a use case of combining 10x Visium with the @PacBio MAS-Seq single-cell kit. No short reads needed. If you missed the story - the webinar recording

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Liz Tseng

@Magdoll

3 years

You can tell a lot about me by just looking at my feet today 😎 #WomenInScience #WomenInSTEM #WomenInScienceDay2021

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Liz Tseng

@Magdoll

5 months

As someone who works in the industry, the skills I learned from getting a PhD that are still relevant 10 years later has nothing to do with writing algorithms or tenure. It is rather, just a mindset and a way of handling hard problems at work and in life. /1

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Liz Tseng

@Magdoll

5 years

I just asked a Q at #gi2019 (cuz @lpachter wants more girls to ask Q) and guess what? my CSHL collaborator, sitting in her office listening in on the talks - emailed me right after and said "HEY I HEARD YOU let's chat tomorrow". So ladies, SPEAK UP.

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Liz Tseng

@Magdoll

3 years

De novo isoform-level phasing using @PacBio Iso-Seq! Years ago I developed IsoPhase (v0) that used the genome to identify SNPs and phase, now we are experimenting w directly going into phasing, which would eliminate the need for a genome! #PlantBiology

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Liz Tseng

@Magdoll

5 months

@PacBio 12/ If the idea of a grant gives you vertigo but instead you are: - Passionate about science - Likes solving problems, no matter where they come from ("intron retention in plants? yes! alternative splicing in alzheimer's brains? of course!") - Wants to do something else in the

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Liz Tseng

@Magdoll

2 years

Going head-to-toe @PacBio today (mask, shirt, bag, socks!) I guess I’m just missing the hat….

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Liz Tseng

@Magdoll

2 years

Measuring polyA length using @PacBio w a modified "PAIso-Seq" protocol, works for 0.5ng of total RNA....😮

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Liz Tseng

@Magdoll

1 year

. @sedlazeck : Sniffles2 benchmark on GIAB outperforms other SV callers; merge to get fully genotyped population VCF! also fast.

GitHub - fritzsedlazeck/Sniffles: Structural variation caller using third generation sequencing

Structural variation caller using third generation sequencing - fritzsedlazeck/Sniffles

github.com

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Liz Tseng

@Magdoll

6 months

What does "full-length (FL) transcript" mean for @PacBio Iso-Seq and how is it determined w #bioinformatics ? In long-read RNA-Seq land, a read with both the 5' and 3' cDNA primer, and the polyA tail preceding the 3' end is determined to be a "full-length" (FL) read. /1

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Liz Tseng

@Magdoll

9 months

The future of #RNA -Seq is now. The Kinnex kits are both a @PacBio company story and a personal story. /1🧵

PacBio

@PacBio

9 months

The future of RNA sequencing is with long reads! Check out these helpful resources on the new Kinnex RNA kits: #PacBio #ASHG23 #ASHG2023

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Liz Tseng

@Magdoll

3 years

Comprehensive @PacBio Iso-Seq breast cancer dataset including tumor samples that contain novel isoforms (that changes ORF) not seen in cell lines! Found 35 alt. splicing events assoc w patient survival. congrats @adeslat :)

A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer

Breast cancer long-read transcriptome profiling reveals patient-enriched isoforms, with implications for disease progression.

www.science.org

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Liz Tseng

@Magdoll

5 years

Just interviewed @sedlazeck and @MedhatHelmy7 on their SV review paper (for my @Medium blog) but we covered so much more ground incl. history of SV, tool dev, postdoc, population scaling...AHHHH why do I have more meetings today I just want to write NOW 😭

Structural variant calling: the long and the short of it - Genome Biology

Recent research into structural variants (SVs) has established their importance to medicine and molecular biology, elucidating their role in various diseases, regulation of gene expression, ethnic...

genomebiology.biomedcentral.com

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Liz Tseng

@Magdoll

4 years

I don't know why I have to say this, but the most effective #bioinformatics strategy to "why something isn't working", sometimes, is to just actually open up the fasta file in a text editor, Ctrl+F to find, look at a handful of sequences by eye, and you usually know what's wrong.

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Liz Tseng

@Magdoll

5 years

Nice review article on history of sequencing + RNA-seq and the use of @PacBio for transcriptome sequencing (Iso-Seq):

Frontiers | Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule...

Advances in transcriptomics have provided an exceptional opportunity to study functional implications of the genetic variability. Technologies such as RNA-Se...

www.frontiersin.org

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Liz Tseng

@Magdoll

6 months

Isoform classification - a largely solved #bioinformatics problem. (hot take? come at me 🌶️) One of the most popular isoform classification tool is SQANTI. Originally published in 2018, SQANTI is now in its 3rd version (SQANTI3) and is also implemented as `pigeon` in @PacBio

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Liz Tseng

@Magdoll

4 years

The Vertebrate Genome Project assembled genomes are now on @GenomeBrowser ! @genomeark @PacBio #bioinformatics

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Liz Tseng

@Magdoll

3 years

My #bioinformatics superpower is discovering other people using (1) wrong primer sequences; (2) wrong primer orientations; (3) wrong file names; (4) using default parameters that don't apply. That, and I discover it faster than most people.

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Liz Tseng

@Magdoll

3 years

What can we learn about the transcript-level changes in hibernating v active brown bears using @PacBio Iso-Seq? Read this preprint by @joannalkelley @JG_Underwood , I and others! Quick thread below /1

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Liz Tseng

@Magdoll

3 years

pepper genome + annotation using @PacBio & Hi-C to look at 3D genome structure

The 3D architecture of the pepper (Capsicum annum) genome and its relationship to function and...

The architecture of topologically associating domains (TADs) varies across plant genomes. Understanding the functional consequences of this diversity requires insights into the pattern, structure,...

www.biorxiv.org

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Liz Tseng

@Magdoll

2 years

Want to know how to get from @PacBio (MAS-Seq) #singlecell Iso-Seq analysis to Seurat + cell clustering? See this #bioinformatics tutorial!

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Liz Tseng

@Magdoll

8 months

How to tell I'm a former computer scientist / bioinformatician - I name my Word docs without spaces and use underscore and capitalization to separate words. XDDDD

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Liz Tseng

@Magdoll

5 years

I’m talking tonight 725pm in #PAGXVIII single cell genomics session on single cell IsoSeq using @PacBio . Come talk to me about what single cell questions can be asked on 🌱 and animals. Talk slides will be online later! #pag2020

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Liz Tseng

@Magdoll

4 years

I hate perl. Can perl just disappear from the world?

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Liz Tseng

@Magdoll

2 years

Using @PacBio Iso-Seq to identify mammalian pseudogenes - most were novel, some have coding potential and have SNPs.

Evolution and function of developmentally dynamic pseudogenes in mammals - Genome Biology

Background Pseudogenes are excellent markers for genome evolution, which are emerging as crucial regulators of development and disease, especially cancer. However, systematic functional characteriz...

genomebiology.biomedcentral.com

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Liz Tseng

@Magdoll

4 years

Amazing preprint out of @hudsonalpha showing using @PacBio HiFi reads solving previously unsolved rare disease! In one case, 35bp duplication of CDKL5 exon 3 resulted in frameshift.

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Liz Tseng

@Magdoll

2 years

Hey there #Bioinformatics folks looking for a job, I have an academic PI friend looking to hire bioinfx talent to work on long read ( @PacBio Iso-Seq) + other omics. International candidates welcome! no job req yet so for now DM me to be connected. RT appreciated ❤️

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Liz Tseng

@Magdoll

3 years

holy shit 1 MIN drosophila assembly and 10 MIN human assembly on @PacBio HiFi O____O

Rayan Chikhi

@RayanChikhi

3 years

Here is our preprint “Minimizer-space de Bruijn graphs”, that will be presented at RECOMB ’21

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Liz Tseng

@Magdoll

3 years

New @PacBio Iso-Seq community tool - IsoTools! Check out the preprint and code #bioinformatics

Long-read transcriptome sequencing analysis with IsoTools

Long-read transcriptome sequencing (LRTS) holds the promise to boost our understanding of alternative splicing. Recent advances in accuracy and throughput have diminished the major limitations and...

www.biorxiv.org

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Liz Tseng

@Magdoll

4 years

Reading the @SangerToL genome book w my kid this morning! Beautiful illustrations by @ATJCagan !

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Liz Tseng

@Magdoll

2 months

From @mrvollger (Stergachis lab): analysis of haplotype-resolved @PacBio HiFi FiberSeq genome reveals >1,000 regulatory elements with haplotype-selective chromatin accessibility (HSCA), with HLA being the most diverse locus. Accurate quantification of chromatin accessibility

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Liz Tseng

@Magdoll

3 years

While I'm going down memory lane today...this is probably the best moments from 10 years ago, when I sang the national anthem for a Mariners game. Ah, when I was young XDDD

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Liz Tseng

@Magdoll

4 years

A small but hopefully still useful potato pan-transcriptome dataset (in which I helped out w the @PacBio Iso-Seq portion). I'm really looking forward to seeing more pan-transcriptomes!

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Liz Tseng

@Magdoll

1 year

Are mixed @PacBio socks a blasphemy? 😝

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Liz Tseng

@Magdoll

9 months

It’s Wednesday.

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Liz Tseng

@Magdoll

2 months

Targeted @PacBio Iso-Seq identifies novel SNCA transcripts in human dopaminergic neurons, many with novel UTRs and encodes novel peptides, and used to design antisense oligonucleotides (ASO) leading to the effective reversal of Parkinson's Disease (PD) pathology

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Liz Tseng

@Magdoll

3 years

Fantastic preprint! Deep @PacBio Iso-Seq+RNA-Seq+mass spec comparative transcriptomics (human + great apes + macaque) finds species-specific isoforms/exonization enriched for immune genes and under positive selection. This is how it's done!

Transcriptome innovations in primates revealed by single-molecule long-read sequencing

Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to...

www.biorxiv.org

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Liz Tseng

@Magdoll

1 month

Microflora Danica: largest microbiome dataset to date using short + long reads for metagenomics, 16S amplion and rRNA operon sequencing of the Danish microbiome. 449 rep samples (14.9 million bacterial and 13.4 million eukaryotic rRNA ~4-4.5kb operon) using @PacBio . This is

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Liz Tseng

@Magdoll

26 days

Eicher: SVbyEye for visualizing multiple genome alignments. #bioinformatics #ISMB2024

GitHub - daewoooo/SVbyEye

Contribute to daewoooo/SVbyEye development by creating an account on GitHub.

github.com

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Liz Tseng

@Magdoll

3 years

I'm giving a @PacBio Iso-Seq webinar tonight ...in Mandarin. The last time I spoke any science in Mandarin was pre-pandemic. Current mood:

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Liz Tseng

@Magdoll

3 years

Korlach presents the (often glossed over but critical) #bioinformatics workflow for @PacBio HiFi genome for SV detection. #AGBT21

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Liz Tseng

@Magdoll

4 years

To @PacBio Iso-Seq users: SQANTI2 is deprecated and replaced by SQANTI3 (). please switch to the new one! #Bioinformatics

GitHub - ConesaLab/SQANTI3: Tool for the Quality Control of Long-Read Defined Transcriptomes

Tool for the Quality Control of Long-Read Defined Transcriptomes - ConesaLab/SQANTI3

github.com

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Liz Tseng

@Magdoll

6 months

Long-read isoform sequencing w @PacBio (Iso-Seq) identified SPARC gene isoform expressed >10,000-fold higher than adjacent non-malignant tissue in pediatric diffuse midline glioma.

Full-length isoform concatenation sequencing to resolve cancer transcriptome complexity - BMC...

Background Cancers exhibit complex transcriptomes with aberrant splicing that induces isoform-level differential expression compared to non-diseased tissues. Transcriptomic profiling using short-read...

bmcgenomics.biomedcentral.com

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Liz Tseng

@Magdoll

5 years

The most unique question I got asked today standing at my Alzheimer’s brain poster: “So this is from postmortem brain, right?” Me: “Uh, yes...?” I mean what is the alternative? Not postmortem brain??!! 🤯😱 #ASHG19

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Liz Tseng

@Magdoll

4 years

Want to find the latest and greatest @PacBio dataset? We've started compiling one here!

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Liz Tseng

@Magdoll

5 months

The new @PacBio Kinnex kits makes long-read RNA sequencing scalable - what's the magic? This animation explains the technology behind Kinnex. Kinnex is based on the MAS-Seq method for concatenating smaller amplicons (cDNA or 16S) into longer fragments that can fully utilize HiFi

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Liz Tseng

@Magdoll

9 months

Come see my @PacBio Kinnex full-length RNA #ASHG23 poster! I’ll be there tomorrow Sat 215-415pm

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Liz Tseng

@Magdoll

3 years

Our preprint for VCFCons is up! We wrote this to generate consensus for @Labcorp SARS-CoV-2 @PacBio sequences. Code is up at CoSa

VCFCons: a versatile VCF-based consensus sequence generator for small genomes

We had developed VCFCons to address urgent need for a robust consensus sequence generator for SARS-CoV-2 viral surveillance, which presented several unique requirements, including: (a) low coverage...

www.biorxiv.org

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Liz Tseng

@Magdoll

7 years

Wrote a quick minimap2 for Iso-Seq guide and did a minimap2 vs GMAP comparison. Would love to have extra pairs of eyes on this, data is public:

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Liz Tseng

@Magdoll

2 years

Paper thread time! Can @PacBio Iso-Seq data be used to identify SNVs and find allele-specfic isoform information? Yes! And here's the list of pubs off top of my head: /1

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Liz Tseng

@Magdoll

4 years

I wrote ANGEL years ago for ORF prediction from long read data that can handle errors (and also handle alternative ORFs). I have mixed feelings about its continuing utility, but this weekend I said heck - I'm updating it to Py3. #Bioinformatics @PacBio

GitHub - PacificBiosciences/ANGEL: Robust Open Reading Frame prediction (ANGLE re-implementation)

Robust Open Reading Frame prediction (ANGLE re-implementation) - PacificBiosciences/ANGEL

github.com

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Liz Tseng

@Magdoll

3 months

Paraphase: a @PacBio #bioinformatics tool for haplotyping segmental duplication genes. Applied to 160 locus, resolved copy numbers, de novo mutations, pseudogenes, low diversity gene example AMY1 as shown below.

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Liz Tseng

@Magdoll

2 years

Congrats to @em_ka_gu & others for publishing ggtranscript (R package for full-length isoform viz)! #bioinformatics @PacBio

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Liz Tseng

@Magdoll

6 years

How many tools had to be created to detect and visualize cancer rearrangement? I interviewed @marianattestad for her SKBR3 work to find out. @PacBio @mike_schatz @sedlazeck