Liz Tseng
@magdoll.bsky.social
Product manager @PacBio / RNA / bioinformatics / aerialist & pole dancer / opinions are my own and do not reflect views of my employer
PangyPlot: a new #bioinformatics tools for visualizing pangenomes that supports linear coordinates and large graphs. Applied to @pacbio.bsky.social HiFi genomes to visualize two cystic fibrosis-relevant region not possible to resolve with short read genomes. www.biorxiv.org/content/10.1...
November 10, 2025 at 6:33 PM
PangyPlot: a new #bioinformatics tools for visualizing pangenomes that supports linear coordinates and large graphs. Applied to @pacbio.bsky.social HiFi genomes to visualize two cystic fibrosis-relevant region not possible to resolve with short read genomes. www.biorxiv.org/content/10.1...
Wonder how @pacbio.bsky.social long read sequencing is transforming how clinical and translational labs approach genomics? Hear from panelists from Myriad Genetics, GeneDx, Karolina and Radboudumc discuss rare disease testing, carrier screening, and more! programs.pacb.com/l/1652/2025-...
October 27, 2025 at 11:58 PM
Wonder how @pacbio.bsky.social long read sequencing is transforming how clinical and translational labs approach genomics? Hear from panelists from Myriad Genetics, GeneDx, Karolina and Radboudumc discuss rare disease testing, carrier screening, and more! programs.pacb.com/l/1652/2025-...
Rarely do I get this excited about a @pacbio.bsky.social Iso-Seq study! 🧠 Come hear how the Tripathy lab used long-read multiomics to study neuron development—finding new isoforms suggesting some non-coding ASD variants may disrupt splicing & protein function. programs.pacb.com/l/1652/2025-...
August 14, 2025 at 5:42 PM
Rarely do I get this excited about a @pacbio.bsky.social Iso-Seq study! 🧠 Come hear how the Tripathy lab used long-read multiomics to study neuron development—finding new isoforms suggesting some non-coding ASD variants may disrupt splicing & protein function. programs.pacb.com/l/1652/2025-...
A once-in-a-decade bloom of Chanel the corpse flower (Amorphophallus Titanum) at the San Francisco Conservatory of Flowers and I caught the very tail end of its 48 hour blooming span! 🌸🌸🌷🌷
July 10, 2025 at 5:36 PM
A once-in-a-decade bloom of Chanel the corpse flower (Amorphophallus Titanum) at the San Francisco Conservatory of Flowers and I caught the very tail end of its 48 hour blooming span! 🌸🌸🌷🌷
Next week! Come learn how @pacbio.bsky.social HiFi enables IGH genotyping and near-full-length TCR/BCR sequencing for immunotherapy research!
programs.pacb.com/l/1652/2025-...
programs.pacb.com/l/1652/2025-...
May 27, 2025 at 9:24 PM
Next week! Come learn how @pacbio.bsky.social HiFi enables IGH genotyping and near-full-length TCR/BCR sequencing for immunotherapy research!
programs.pacb.com/l/1652/2025-...
programs.pacb.com/l/1652/2025-...
@pacbio.bsky.social instrument lounge at PRISM San Francisco event today! Great talks this morning and now we’re moving into parallel workshops.
May 7, 2025 at 6:00 PM
@pacbio.bsky.social instrument lounge at PRISM San Francisco event today! Great talks this morning and now we’re moving into parallel workshops.
It's @pacbio.bsky.social fairy tale Friday!
Once upon a time, you do lots of PCRs to screen different ataxia genes.
Now with PureTarget, you can do 20 genes at once, get repeat lengths, repeat sequences, and even methylation patterns!
Once upon a time, you do lots of PCRs to screen different ataxia genes.
Now with PureTarget, you can do 20 genes at once, get repeat lengths, repeat sequences, and even methylation patterns!
March 21, 2025 at 12:49 PM
It's @pacbio.bsky.social fairy tale Friday!
Once upon a time, you do lots of PCRs to screen different ataxia genes.
Now with PureTarget, you can do 20 genes at once, get repeat lengths, repeat sequences, and even methylation patterns!
Once upon a time, you do lots of PCRs to screen different ataxia genes.
Now with PureTarget, you can do 20 genes at once, get repeat lengths, repeat sequences, and even methylation patterns!
"Don't just focus on gene expressions". Instead, you might find common mis-splicing patterns that aren't derived from SF mutations, is associated with prognosis, and may have therapeutic potential.
Intrigued? Register for @pacbio.bsky.social webinar next week! programs.pacb.com/l/1652/2025-...
Intrigued? Register for @pacbio.bsky.social webinar next week! programs.pacb.com/l/1652/2025-...
March 11, 2025 at 7:30 PM
"Don't just focus on gene expressions". Instead, you might find common mis-splicing patterns that aren't derived from SF mutations, is associated with prognosis, and may have therapeutic potential.
Intrigued? Register for @pacbio.bsky.social webinar next week! programs.pacb.com/l/1652/2025-...
Intrigued? Register for @pacbio.bsky.social webinar next week! programs.pacb.com/l/1652/2025-...
Sunday cafe reading! I sort of “won” this book from a recent @pacbio.bsky.social internal event and I’m greatly enjoying it! So much to think about on pursuing greatness, offering hospitality, and relationship management.
March 10, 2025 at 1:27 AM
Sunday cafe reading! I sort of “won” this book from a recent @pacbio.bsky.social internal event and I’m greatly enjoying it! So much to think about on pursuing greatness, offering hospitality, and relationship management.
@pacbio.bsky.social Vega in the flesh today at Stanford!! 😁
March 4, 2025 at 10:35 PM
@pacbio.bsky.social Vega in the flesh today at Stanford!! 😁
Bay area folks! Want a chance to see the new @pacbio.bsky.social benchtop Vega in person? Chat with me and other PacBio folks about HiFi sequencing? We're hosting a Vega showcase + office hour tomorrow at Stanford! Come say hi!
programs.pacb.com/l/1652/2025-...
programs.pacb.com/l/1652/2025-...
March 3, 2025 at 11:05 PM
Bay area folks! Want a chance to see the new @pacbio.bsky.social benchtop Vega in person? Chat with me and other PacBio folks about HiFi sequencing? We're hosting a Vega showcase + office hour tomorrow at Stanford! Come say hi!
programs.pacb.com/l/1652/2025-...
programs.pacb.com/l/1652/2025-...
Happy Monday! Let's start this week with fairy tales!
ONCE UPON A TIME extracting high molecular weight (HMW) DNA was difficult. But now, with @pacbio.bsky.social Nanobind extraction kits. you get HMW DNA in, and beautiful long reads -> genome assemblies out! 💫⭐🧪🧬
www.pacb.com/products-and...
ONCE UPON A TIME extracting high molecular weight (HMW) DNA was difficult. But now, with @pacbio.bsky.social Nanobind extraction kits. you get HMW DNA in, and beautiful long reads -> genome assemblies out! 💫⭐🧪🧬
www.pacb.com/products-and...
March 3, 2025 at 5:50 PM
Happy Monday! Let's start this week with fairy tales!
ONCE UPON A TIME extracting high molecular weight (HMW) DNA was difficult. But now, with @pacbio.bsky.social Nanobind extraction kits. you get HMW DNA in, and beautiful long reads -> genome assemblies out! 💫⭐🧪🧬
www.pacb.com/products-and...
ONCE UPON A TIME extracting high molecular weight (HMW) DNA was difficult. But now, with @pacbio.bsky.social Nanobind extraction kits. you get HMW DNA in, and beautiful long reads -> genome assemblies out! 💫⭐🧪🧬
www.pacb.com/products-and...
A coworker sent me this this morning and cracked me up so much! 🧬🧪
xkcd.com/3056/
xkcd.com/3056/
February 28, 2025 at 4:51 PM
A coworker sent me this this morning and cracked me up so much! 🧬🧪
xkcd.com/3056/
xkcd.com/3056/
For the past few years I started doing “New Year Key Words”. I reflect on what the past year taught me and come up with three words (or “mantras”) that I keep close to me as I navigate through a new year.
For 2025, I choose TEACH, COMMUNITY, and CREATION /1
For 2025, I choose TEACH, COMMUNITY, and CREATION /1
January 15, 2025 at 11:23 PM
For the past few years I started doing “New Year Key Words”. I reflect on what the past year taught me and come up with three words (or “mantras”) that I keep close to me as I navigate through a new year.
For 2025, I choose TEACH, COMMUNITY, and CREATION /1
For 2025, I choose TEACH, COMMUNITY, and CREATION /1
Blooper reel for @pacbio.bsky.social "PacBio PI Chronicles and a bit about "what do you do as a product manager [in a biotech sequencing company]"?
🧵 /1
🧵 /1
January 7, 2025 at 10:10 PM
Blooper reel for @pacbio.bsky.social "PacBio PI Chronicles and a bit about "what do you do as a product manager [in a biotech sequencing company]"?
🧵 /1
🧵 /1
Happy new year! Starting 2025 with a clip the pilot episode of the "PacBio PI Chronicles". Peter is working on a grant (surprise....life of a professor!) and Mary suggests looking into @pacbio.bsky.social HiFi for covering those repeat expansion regions. Full episode: www.youtube.com/watch?v=FB6Z...
January 3, 2025 at 5:35 PM
Happy new year! Starting 2025 with a clip the pilot episode of the "PacBio PI Chronicles". Peter is working on a grant (surprise....life of a professor!) and Mary suggests looking into @pacbio.bsky.social HiFi for covering those repeat expansion regions. Full episode: www.youtube.com/watch?v=FB6Z...
Tomorrow! Hear UCL researcher use @pacbio.bsky.social WGS + RNA-Seq to advance Parkinson's Disease (Ryten's group published my fav preprint of 2024)
programs.pacb.com/l/1652/2024-...
programs.pacb.com/l/1652/2024-...
December 16, 2024 at 8:46 PM
Tomorrow! Hear UCL researcher use @pacbio.bsky.social WGS + RNA-Seq to advance Parkinson's Disease (Ryten's group published my fav preprint of 2024)
programs.pacb.com/l/1652/2024-...
programs.pacb.com/l/1652/2024-...
5/ what about the Kinnex concatenation? How does that affect this Iso-Seq pipeline?
Kinnex kits such as the Kinnex full-length RNA kit concatenated full-length cDNAs into an ordered array to sequence with HiFi to increase cDNA yield.
HiFi reads are segmented skera into individual S-reads.
Kinnex kits such as the Kinnex full-length RNA kit concatenated full-length cDNAs into an ordered array to sequence with HiFi to increase cDNA yield.
HiFi reads are segmented skera into individual S-reads.
February 23, 2024 at 2:56 AM
5/ what about the Kinnex concatenation? How does that affect this Iso-Seq pipeline?
Kinnex kits such as the Kinnex full-length RNA kit concatenated full-length cDNAs into an ordered array to sequence with HiFi to increase cDNA yield.
HiFi reads are segmented skera into individual S-reads.
Kinnex kits such as the Kinnex full-length RNA kit concatenated full-length cDNAs into an ordered array to sequence with HiFi to increase cDNA yield.
HiFi reads are segmented skera into individual S-reads.
4/ from FLNC reads we typically then recommend `isoseq cluster` for de novo isoform-level clustering before mapping, collapse, and annotation (which will be a future topic!)
February 23, 2024 at 2:53 AM
4/ from FLNC reads we typically then recommend `isoseq cluster` for de novo isoform-level clustering before mapping, collapse, and annotation (which will be a future topic!)
3/ The tool `isoseq refine` (1) removes the polyA tail and (2) filters out artificial concatemers.
The output of `isoseq3 refine` are full-length, non-concatemer (FLNC) reads.
The output of `isoseq3 refine` are full-length, non-concatemer (FLNC) reads.
February 23, 2024 at 2:53 AM
3/ The tool `isoseq refine` (1) removes the polyA tail and (2) filters out artificial concatemers.
The output of `isoseq3 refine` are full-length, non-concatemer (FLNC) reads.
The output of `isoseq3 refine` are full-length, non-concatemer (FLNC) reads.
2/ The tool `lima` can trim away the cDNA primers and also use the asymmetry of the 5'/3' to orient the read to the transcript-sense. Use the `lima --isoseq` option to turn on this functionality.
February 23, 2024 at 2:52 AM
2/ The tool `lima` can trim away the cDNA primers and also use the asymmetry of the 5'/3' to orient the read to the transcript-sense. Use the `lima --isoseq` option to turn on this functionality.
1/ What does "full-length (FL) transcript" mean for @pacbio.bsky.social 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.
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.
February 23, 2024 at 2:52 AM
1/ What does "full-length (FL) transcript" mean for @pacbio.bsky.social 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.
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.
4/ here are the main isoform categories. Mainly, FSM/ISMs are "known" while "NIC/NNC" are the "novels".
FSM - matches reference on all splice junctions (SJ)
ISM - matches ref on SJs but alt first/last exons
NIC - novel isoform but all SJs are known
NNC - novel isoform, at least one SJ is new
FSM - matches reference on all splice junctions (SJ)
ISM - matches ref on SJs but alt first/last exons
NIC - novel isoform but all SJs are known
NNC - novel isoform, at least one SJ is new
February 16, 2024 at 9:46 PM
4/ here are the main isoform categories. Mainly, FSM/ISMs are "known" while "NIC/NNC" are the "novels".
FSM - matches reference on all splice junctions (SJ)
ISM - matches ref on SJs but alt first/last exons
NIC - novel isoform but all SJs are known
NNC - novel isoform, at least one SJ is new
FSM - matches reference on all splice junctions (SJ)
ISM - matches ref on SJs but alt first/last exons
NIC - novel isoform but all SJs are known
NNC - novel isoform, at least one SJ is new
Completed my first UK driving experience. A local asked me what my cultural shock is and my answer is:
Roundabouts. SO MANY ROUNDABOUTS!!!!!!
Also that people park the cars in any orientation alongside the road instead of always facing the direction of the lane they’re on.
Roundabouts. SO MANY ROUNDABOUTS!!!!!!
Also that people park the cars in any orientation alongside the road instead of always facing the direction of the lane they’re on.
November 26, 2023 at 7:29 AM
Completed my first UK driving experience. A local asked me what my cultural shock is and my answer is:
Roundabouts. SO MANY ROUNDABOUTS!!!!!!
Also that people park the cars in any orientation alongside the road instead of always facing the direction of the lane they’re on.
Roundabouts. SO MANY ROUNDABOUTS!!!!!!
Also that people park the cars in any orientation alongside the road instead of always facing the direction of the lane they’re on.
Sunday musing for #WomenInSTEM:
Be honest about what you are truly available for. Just because others ask you doesn’t mean you have to say yes. This could mean saying no to:
- analyzing data for others
- “helping” out an experiment
- writing
- volunteering for a committee
Be honest about what you are truly available for. Just because others ask you doesn’t mean you have to say yes. This could mean saying no to:
- analyzing data for others
- “helping” out an experiment
- writing
- volunteering for a committee
November 25, 2023 at 7:10 PM
Sunday musing for #WomenInSTEM:
Be honest about what you are truly available for. Just because others ask you doesn’t mean you have to say yes. This could mean saying no to:
- analyzing data for others
- “helping” out an experiment
- writing
- volunteering for a committee
Be honest about what you are truly available for. Just because others ask you doesn’t mean you have to say yes. This could mean saying no to:
- analyzing data for others
- “helping” out an experiment
- writing
- volunteering for a committee