Shunhua Han
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shunhuahan.bsky.social
Shunhua Han
@shunhuahan.bsky.social
1.4K followers 680 following 22 posts
Bioinformatics Scientist at Illumina. I work on finding challenging variants. Views are my own.

https://orcid.org/0000-0002-8605-7547
Posts Replies Media Videos
shunhuahan.bsky.social
Really great talk!
sinamajidian.bsky.social Sina Majidian @sinamajidian.bsky.social · 22d
Fantastic talk by @vikramshivakumar.bsky.social Mumemto—Scalable multi-MUM finding for pangenomes
Papers biorxiv.org/content/10.1101/2025.05.20.654611 & doi.org/10.1186/s13059-025-03644-0
Code: github.com/vikshiv/mume...
Very efficient pangenome visualization tool, revealing synteny and variations!
Figure 1: (A) Anchor-based merging requires a common sequence (red) present in each partition. Multi-MUMs are merged by identifying overlaps between partition-specific matches in the anchor coordinate space, and a uniqueness threshold determines if a MUM is still unique in each partition after truncation. (B) String-based merging enables compu- tation of multi-MUMs between partitions without a common sequence. An example tree (left) is shown, highlighting the use case where partial multi-MUMs specific to internal nodes (starred) can be computed by merging subclade-based partitions up a tree. (right) MUM overlaps are computed by running Mumemto on the MUM sequences, and the uniqueness threshold array ensures overlaps remain unique across the merged dataset. (C) An example Burrows-Wheeler Transform (BWT), matrix (BWM), and Longest Com- mon Prefix (LCP) array, with sequence IDs for each suffix shown (ID). A non-maximal unique match (UM) is shown, and the uniqueness threshold for this match is found us- ing the flanking LCP values. (D) A partial multi-MUM (in blue) is found in all-but-one sequence (excluded in red). Using two anchor sequences (red and orange), all-but-one partial MUMs can be computed using an augmented anchor-based merging method (sec- tion 2.6).
November 6, 2025 at 1:33 AM
shunhuahan.bsky.social
If you are interested in medically relevant and challenging genes (e.g., SMN1/2, PMS2, NCF1, STRC...). I encourage you to watch this talk that our collaborator at GeneDx gave at ASHG 2025.

You can watch it here: www.illumina.com/events/webin....

The talk starts at 31:57 and runs through 50:41.
Redefining the limits of what’s possible: Sequencing reimagined
Watch our on-demand webinar to see how Illumina innovations are expanding what's possible in genome sequencing.
www.illumina.com
October 24, 2025 at 2:33 AM
Reposted by Shunhua Han
yekaixiong.bsky.social
We @uga_genetics are hiring a TT assistant professor in Human Genetics to investigate how genetic makeup influences an individual’s risks for diseases or responses to drugs and therapies. All research
approaches will be considered. Please RT. ugajobsearch.com/postings/456597
October 21, 2025 at 8:19 PM
Reposted by Shunhua Han
horacezhl.bsky.social
New paper! We characterized the breeding system elements (number of breeders, relatedness, reproductive skew) of fire ant using data from a long-term rearing study combined with data from previous studies. Open access at: onlinelibrary.wiley.com/doi/full/10....
A Comprehensive Account of the Breeding Systems of the Fire Ant Solenopsis invicta
We comprehensively characterized the breeding system of polygyne fire ant colonies by tracking parentage, relatedness, and supergene genotypes in a large-scale, longitudinal experiment. Our results r....
onlinelibrary.wiley.com
October 5, 2025 at 3:25 AM
Reposted by Shunhua Han
heidirehm.bsky.social
Looking forward to another great AGBT-Precision Health meeting in San Diego Sept 8-10. Abstracts due June 30th. Hope to see you there! We'll have an increased focus on rare disease and AI in genomics this year. #AGBTPH25 www.agbtprecisionhealth.org
HOME | AGBT Precision Health
www.agbtprecisionhealth.org
June 19, 2025 at 6:55 PM
Reposted by Shunhua Han
bioinfoadv.bsky.social
🧬 Now in Bioinformatics Advances: "Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications."

Explore the full paper here: https://doi.org/10.1093/bioadv/vbaf071

Authors include: @ribozyme.bsky.social, @shunhuahan.bsky.social
April 21, 2025 at 2:27 PM
shunhuahan.bsky.social
Here is a sneak peak of the new sequencing technology I have been working on together with many others. Much more to come in 2025!

www.illumina.com/science/geno...
Introducing constellation mapped read technology
Constellation technology utilizes a highly simplified NGS workflow that enables on-flow-cell library prep that completely eliminates standard library prep prior to sequencing Standard cluster generati...
www.illumina.com
December 21, 2024 at 4:56 PM
Reposted by Shunhua Han
natureportfolio.nature.com
One of the biggest questions we get is when will our journals be here. We thank you for your patience.

You can now follow our journals with this starter pack!
December 18, 2024 at 2:57 PM
Reposted by Shunhua Han
penghe.bsky.social
🔬 Hiring: Computational Biology Postdoc @UCSF!

to develop:
1️⃣ Novel deep learning models for spatial/single-cell multiomics
2️⃣ Single-cell analyses across development & disease
3️⃣ Open-source tools for the broader community

Apply here: opportunities.ucsf.edu/content/open...

#CompBio #PostdocJobs
Open Postdoctoral Position in Computational Genomics and Systems Biology
opportunities.ucsf.edu
December 11, 2024 at 4:36 AM
Reposted by Shunhua Han
suragnair.bsky.social
We are hiring an intern to work with our team at Genentech next summer, on exciting projects related to deep learning for DNA/RNA sequences. Please share and apply! roche.wd3.myworkdayjobs.com/ROG-A2O-GENE...
2025 Summer Intern - Biology Research | AI Development
2025 Summer Intern - Biology Research | AI Development Department Summary At Genentech Research & Early Development (gRED) we have initiated an exciting journey to bring together and further stren...
roche.wd3.myworkdayjobs.com
December 5, 2024 at 4:18 AM
Reposted by Shunhua Han
aaronquinlan.bsky.social
Biology of Genomes 2025 is coming up:
- meeting dates: May 6 - 10, 2025
- abstract deadline: Feb 14, 2025
We hope to see you there for another great meeting with a fantastic speaker lineup!

meetings.cshl.edu/meetings.asp...
Biology of Genomes
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
meetings.cshl.edu
December 3, 2024 at 7:21 PM
Reposted by Shunhua Han
aylwyn-scally.bsky.social
Applications open for several research positions here in Cambridge including evolutionary genetics, genomics and population genetics. www.jobs.cam.ac.uk/job/49389/
Associate Professor / Professor of Evolutionary Genomics - Job Opportunities - University of Cambridge
Associate Professor / Professor of Evolutionary Genomics in the Department of Genetics at the University of Cambridge.
www.jobs.cam.ac.uk
December 2, 2024 at 12:30 PM
shunhuahan.bsky.social
Night sky at Joshua Tree NP. Well charged thanksgiving week.
December 1, 2024 at 12:40 AM
Reposted by Shunhua Han
alexis-verger.cpesr.fr
Look who's here
@pnas.org ✔️
@science.org ✔️
@naturecellbiology.bsky.social ✔️
@natrevgenet.bsky.social ✔️
@naturebiotech.bsky.social ✔️
@naturemicrobiol.bsky.social ✔️
@naturechemistry.bsky.social ✔️
@genesdev.bsky.social ✔️
@cellchembiol.bsky.social ✔️
@genomeresearch.bsky.social ✔️
@jcellbiol.bsky.social ✔️
November 25, 2024 at 1:47 PM
Reposted by Shunhua Han
rena-ren.bsky.social
The new Dr. Hailing Shi’s lab at @Emory is hiring at all levels! Hailing is so knowledge and such a wonderful person to work with! Please check out the lab description here. #newPI
November 23, 2024 at 7:21 PM
Reposted by Shunhua Han
jeremycours.bsky.social
First post on Bluesky, let’s share some websites offering many free illustrations for scientific figures 🖼️ 🧪 🌍 :

scidraw.io

bioart.niaid.nih.gov

www.phylopic.org

More well known but very nice though: www.freepik.com
SciDraw | Scientific Drawings
SciDraw - an open repository of science drawings
scidraw.io
November 23, 2024 at 6:57 AM
shunhuahan.bsky.social
Our group is hiring a senior bioinformatics scientist on early R&D prototyping (novel algorithm development). Lots of very cool projects to work on. Let me know if you are interested!

illumina.wd1.myworkdayjobs.com/en-US/illumi...
Senior Bioinformatics Scientist
What if the work you did every day could impact the lives of people you know? Or all of humanity? At Illumina, we are expanding access to genomic technology to realize health equity for billions of pe...
illumina.wd1.myworkdayjobs.com
November 22, 2024 at 11:13 PM
Reposted by Shunhua Han
dicksonlab.bsky.social
Open-rank tenure track positions in computational biology! Come work with a gaggle of great colleagues in the CMSE department at Michigan State! #msu #cmse #compbio #bioinformatics #genomics #BioSky

careers.msu.edu/cw/en-us/job...
MSU Careers Details - Ast/Asc/Full Professor - Tenure System
careers.msu.edu
November 21, 2024 at 5:45 PM
shunhuahan.bsky.social
So cool…
November 21, 2024 at 6:02 PM
Reposted by Shunhua Han
humanpangenome.bsky.social
🔍The Human Genome Projects Next Chapter 🔍
🌍 The Human Genome Project was a historic milestone, providing a reference for countless discoveries in human genetics.
Yet still... gaps remained, particularly around human diversity and complex regions of the genome.
November 21, 2024 at 4:26 PM
Reposted by Shunhua Han
jchrispires.bsky.social
Make your own Google Scholar word cloud! (from shiny.rcg.sfu.ca/u/rdmorin/sc...) #Brassica #Plant #Genome #Evolution #Polyploidy #Phylogeny 🧪
February 5, 2024 at 1:49 AM
Reposted by Shunhua Han
psychgenomics.bsky.social
This is very interesting and highly relevant paper to clinical genetics and rare disease researchers. I wrote the accompanying News & Views piece. Free sharing link here: rdcu.be/d0VlK
November 20, 2024 at 11:11 PM
shunhuahan.bsky.social
I really enjoy this immersive webpage on works coming out of the Human Cell Atlas. Journals ought to create more resources like this for science education.

www.nature.com/immersive/d4...
The Human Cell Atlas: towards a first draft atlas
In a collection of research articles and related content, the Human Cell Atlas consortium presents tools, data and ideas towards the generation of their first draft atlas of cells in the human body.
www.nature.com
November 21, 2024 at 5:08 AM
Reposted by Shunhua Han
smcgrath.phd
New tool that helps you discover new accounts based off who you already follow.
#AcademicSky 🩺🖥️🧬
Bluesky Network Analyzer
Find accounts that you don't follow (yet) but are followed by lots of accounts that you do follow.
bsky-follow-finder.theo.io
November 18, 2024 at 2:25 AM
Reposted by Shunhua Han
sethabramson.bsky.social
I learned some stuff about Bluesky I did not know by reading this.

Maybe worth passing it on to others so we can all start getting the full benefit of the 🦋.
Here’s some cool stuff you can do with Bluesky
It’s not just an Alf pics repository.
www.theverge.com
November 17, 2024 at 8:55 AM