Scientist, Oncology Bioinformatics at @moderna_tx. PhD in Computational and Systems Biology from @WUSTLdbbs. Genomics 🤘.
Taipei
Joined September 2012
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Liang-Bo Wang retweeted
Today Cell, Cancer Cell and Cell Reports Medicine are pleased to publish the 1st wave of Pan-#Cancer multiomics papers looking at over 1000 patients across 10 #tumor types from @theNCI Clinical Proteomic Tumor Analysis Consortium #CPTAC (1/n) @Cancer_Cell @CellRepMed #openaccess
Liang-Bo Wang retweeted
We are excited to announce a collection of new human reference genome sequences that reflect much more global diversity!
nature.com/articles/s41586-0…
Liang-Bo Wang retweeted
webR v0.1.0 has just been released! I'm super excited to see what people create by using webR in their own projects 😃. The docs are at docs.r-wasm.org and I've written an introductory blog post talking more about the kind of things webR can do at tidyverse.org/blog/2023/03/w….
Liang-Bo Wang retweeted
english.cw.com.tw/article/ar…
Thanks to Commonwealth Magazine @CWM_en for publishing a summary version of my article detailing my experience of becoming a Taiwanese citizen as a Taiwan Gold Card holder. Please share it forward to those who may benefit from it. Thank you
Liang-Bo Wang retweeted
Our single-cell MPRA paper is finally out! Super excited about the potential of this technology to study cell-type specific gene regulation 🥰
Out today in @NatureGenet, our group’s single-cell MPRA technology for testing activities of gene regulatory elements in whole tissues.
Congrats to Siqi Zhao and the rest of the crew for their great work!
nature.com/articles/s41588-0…
Liang-Bo Wang retweeted
We are delighted to share our work, now available in
@Nature:
nature.com/articles/s41586-0…
Our scoring system can be accessed here: kinase-library.phosphosite.o…
Coming soon --> the tyrosine kinome and an improved system with many new functionalities & features!
#TheKinaseLibrary #KL
Liang-Bo Wang retweeted
Our paper on insulators is out on Biorxiv! We tested the activity of insulators across thousands of genomic locations to figure out where insulators function. Oh, and I successfully defended today :) biorxiv.org/content/10.1101/…
I converted a ensembldb EnsDb SQLite db to DuckDB and saw a nice speedup (4-6x) in genome-wide queries!
DuckDB's filesize is smaller too (index not needed), and it can be even smaller by offloading tables to external compressed parquet files (still 3x speedup).
ALT Comparison of the time to extract genome-wide data using ensembl's function fiveUTRsByTranscriptfrom() from EnsDB databases in different SQLite and DuckDB backends.
Gene-specific lookup using DuckDB is indeed slower than SQLite. This is expected because SQLite w. index is designed to retrieve specific rows fast.
But since the query takes < 100ms to run, performance hit shouldn't be too bad unless we run this kind of queries in a loop.
ALT Comparison of the time to query gene-specific gene annotations from ensembldb using different SQLite and DuckDB databases
Thanks to DuckDB's R client implementing DBI and ensembldb taking a standard DBI connection to create an EnsDB instance, it's straightforward to replace SQLite with DuckDB.
I had fun using DuckDB :) More details about this exercise at
blog.liang2.tw/posts/2022/10…
I made a presentation at my local #bioinfo meetup about #snakemake and how to best utilize this #workflow management tool as a researcher. The slides are available at blog.liang2.tw/2022Talk-snak… details👇🏼
ALT Cover for my presentation titled "Snakemake—simple data processing for researcher"
Besides data processing pipeline, I also enjoyed managing my personal research projects using Snakemake (eg, data freeze, analyses, and figures). I will recommend making the scripts reproducible first before assembling everything in a pipeline.
Overall, my presentation summed up my experience using Snakemake during my PhD. It's been one of my best investment in bioinformatics tools that greatly boosted my productivity 😎
If this has piqued your interest, check out the official resources at snakemake.github.io/
Liang-Bo Wang retweeted
Finally sharing this collaborative work with my amazing labmates Avi and Siqi! We asked how chromosome position and cellular environments impact gene expression noise by developing a new single-cell method (with a genomicsy name just because) 😉
biorxiv.org/content/10.1101/…
Liang-Bo Wang retweeted
I designed this cover for my PhD thesis using #DALL-E and #StableDiffusion, I'm quite happy with the result!
Took a few steps to combine the strengths of both engines, I found SD: beautiful images, DALLE: gets the story right; look at the steps below: (1/5+2)
Liang-Bo Wang retweeted
After more than two years of working on this project, we are delighted to share our effort in harmonizing the tumor microenvironment (TME) of glioblastoma (GB) at single-cell resolution and providing insights into the tumor architecture (biorxiv.org/cgi/content/shor…).
Details 🧵👇🏼 1/N
Liang-Bo Wang retweeted
‼️ ONLINE NOW @NatureGenet
📰 Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer
🧑🏾🤝🧑🏻 Li Ding @reykajayasinghe @DeNardoLabWUSM and colleagues
⬇️
go.nature.com/3AEvt3n
Liang-Bo Wang retweeted
There are different versions of the human genome annotation but which do you use?
The Matched Annotation from @NCBI and EMBL-EBI (MANE) collaboration is the answer and brings new meaning to the phrase: two heads are better than one.
ebi.ac.uk/about/news/researc…
