Liang-Bo Wang

Scientist, Oncology Bioinformatics at @moderna_tx. PhD in Computational and Systems Biology from @WUSTLdbbs. Genomics 🤘.

[Cell @CellCellPress]

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

[Human Pangenome Reference Consortium @HumanPangenome]

We are excited to announce a collection of new human reference genome sequences that reflect much more global diversity!
https://t.co/a39cFG8dOu

[George Stagg @gwstagg]

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 https://t.co/VhzF2Co3t4 and I've written an introductory blog post talking more about the kind of things webR can do at https://t.co/56ficIti3l.

[Sam Taiwan @SamKTaiwan]

https://t.co/1DX75mydT7

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

[clarice @claricehongky]

Our single-cell MPRA paper is finally out! Super excited about the potential of this technology to study cell-type specific gene regulation 🥰

[Cantley Lab @CantleyLab]

We are delighted to share our work, now available in
@Nature:

https://t.co/E5FBUsH2YW

Our scoring system can be accessed here: https://t.co/uPmrvbqD50

Coming soon --> the tyrosine kinome and an improved system with many new functionalities & features!

#TheKinaseLibrary #KL

[clarice @claricehongky]

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 :) https://t.co/hRIdU2ej3Z

[Liang-Bo Wang @lbwang2]

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
https://t.co/NaKsEmkpNZ

[Liang-Bo Wang @lbwang2]

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).

[Liang-Bo Wang @lbwang2]

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.

[Liang-Bo Wang @lbwang2]

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 https://t.co/ycgK0fYZrr

[Liang-Bo Wang @lbwang2]

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 https://t.co/0QVohK1GQV details👇🏼

[Liang-Bo Wang @lbwang2]

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.

[clarice @claricehongky]

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) 😉
https://t.co/V7GKSxOZmy

[Wouter van Amsterdam @WvanAmsterdam]

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)

[Cristian Ruiz Moreno @CristianCRuizM]

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 (https://t.co/AUYBcfWTmN).
Details 🧵👇🏼 1/N

[Nature Genetics @NatureGenet]

‼️ 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
⬇️
https://t.co/oh9DZDAsrm

[EMBL-EBI @emblebi]

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.

https://t.co/piRx08NP2b