Jaebeom Kim

Developing software to analyze biological data at Seoul National University with @thesteinegger

[Jaebeom Kim @jbeom_kim]

Easy taxonomic profiling with the Metabuli App! Explore your samples with publication-ready Sankey and Krona plots. We accelerated Metabuli further, classifying 2x22M reads vs. GTDB in just 43 min on a MacBook Pro M2. 🧵1/4
🚀https://t.co/cxCTrraDP9
📄https://t.co/94BP8OD7VV

[ASCS2026 @iscb_ascs]

🧬 SAVE THE DATE! 💻
The 5th Asian Student Council Symposium (#ASCS2026) is happening!

Join the ultimate student-led gathering bridging the gap between biology and code. 🚀

📅 When: November 17, 2026
📍 Where: Yonsei University, Seoul, South Korea (In person)
👇 (1/5)

[Jaebeom Kim @jbeom_kim]

We’re thrilled to launch the first @RSG_KOREA webinar!
Open to anyone, anywhere — all are welcome.
Join us and follow @RSG_KOREA to stay updated on future events.

[ISCB RSG KOREA @RSG_KOREA]

We are thrilled to host our first webinar. The speaker is our faculty advisor, Martin Steinegger!
🗓Time: 17:00–18:00(KST), Mon, June 23rd (Online)
🔗Register: https://t.co/T4d4qjAif7
🧾Certificates will be provided.

[ISCB RSG KOREA @RSG_KOREA]

We are thrilled to host our first webinar. The speaker is our faculty advisor, Martin Steinegger!
🗓Time: 17:00–18:00(KST), Mon, June 23rd (Online)
🔗Register: https://t.co/T4d4qjAif7
🧾Certificates will be provided.

[Jaebeom Kim @jbeom_kim]

🚀 New Metabuli DB is out! It contains quality-filtered GTDB, RefSeq viruses, and the human T2T. Prokaryotes follow the GTDB; viruses and the human follow NCBI taxonomy. Download it and expand with genomes of your choice using "updateDB" command. https://t.co/ZrPPTEYQVD

[촛불행동 @candlemove]

오늘 국회 앞 인파

2번이고, 3번이고 탄핵 가결될 때까지
끝까지 함께 싸워주십시오.

저희도 흔들리지 않고 탄핵만을 향해 가겠습니다.

부결 시 내일(8일) 오후 3시, 다시 국회 앞으로 모여주십시오.

시간은 변경될 수 있습니다. 자세한 공지는 계정 메인트에 있는 공식 공지 <촛불 n호>를 확인해주시길 바랍니다.

[Yazhini Arangasamy @yazhiniav]

Big thanks to @SoedingL @cshlmeetings @MSCActions for giving an opportunity to share my research work.

[Jaebeom Kim @jbeom_kim]

It was a great honor to give a talk infront of researchers leading the microbiome field 😁 I really hope to join #cshlmbiome again !!

[Yan Shao @yan__shao]

Excited to be speaking @cshlmeetings #cshlmbiome this week about our latest work on the neonatal gut microbiome—just out last month in @NatureMicrobiol

https://t.co/vUSIoEycvH

[Yazhini Arangasamy @yazhiniav]

For anyone looking to classify metagenomic sequences, Metabuli from @thesteinegger is the tool for you! Big thanks to @cshlmeetings for organizing the microbiome meeting.

[Asaf Levy אסף לוי اسف ليڤي @AsafLevyHUJI]

You can always trust @thesteinegger to select the most informative names to his useful databases!
@milot_mirdita

#cshl_microbiome

[Yazhini Arangasamy @yazhiniav]

@milot_mirdita just delivered an excellent talk @cshlmeetings covering viral protein structure database, homology detection, multi-protein complex alignment and multiple protein alignment using 3D structures. Awesome collaborations lead to impactful work! @thesteinegger @SoedingL

[Quanta Magazine @QuantaMagazine]

In 1956, 26-year-old Edgar Dijkstra invented a classic path-finding algorithm while out with his fiancée at a café in Amsterdam. It all happened in his head: “Without pencil and paper you are almost forced to avoid all avoidable complexities,” he said. https://t.co/hvFDiI6wy5

[Yun S. Song @yun_s_song]

Antibodies are highly diverse, but most possible sequences are unstable or polyreactive. In this work led by @milind_jagota, we propose a new source of data for modeling constraints from these properties. Our models show clear improvements in predicting antibody dysfunction.(1/n)

[Valerio Capraro @ValerioCapraro]

Just published in @Nature!

Research by @GoogleDeepMind including Nobel Laureate @demishassabis introduces a novel technique for reliably identifying LLM-generated content.

At its core, this approach subtly alters the next-token sampling process to introduce minor adjustments into the distribution of generated text.

These slight modifications embed a “signature” in the LLM-generated text that would be nearly invisible to a human reader but detectable using specific statistical tools.

A major advantage of this method is its efficiency: detection doesn’t require resource-intensive computations or direct access to the underlying LLM, which is often proprietary.

Full paper: https://t.co/IFgC4YLhPt

[Jaebeom Kim @jbeom_kim]

I'm excited to share that a pipeline I prototyped during my undergrad is now available as a preprint!
COmapper maps meiotic crossover sites using ONT reads extracted from pollen!
Simply put, it detects transitions from maternal to paternal SNPs in pollen genomes of F1 hybrids.

[Kyuha Choi @Kyuha_C]

Excited to share our preprint titled: "COmapper: High-resolution mapping of meiotic crossovers by long-read sequencing in Arabidopsis" on BioRxiv!
https://t.co/cBZLqu8N5f
COmapper enables high-resolution CO maps from F1 hybrid pollen and F2 seedlings using nanopore sequencing.

[Kyuha Choi @Kyuha_C]

Excited to share our preprint titled: "COmapper: High-resolution mapping of meiotic crossovers by long-read sequencing in Arabidopsis" on BioRxiv!
https://t.co/cBZLqu8N5f
COmapper enables high-resolution CO maps from F1 hybrid pollen and F2 seedlings using nanopore sequencing.

[Jaebeom Kim @jbeom_kim]

@shenwei356 Many congratulations !! I really like your taxonkit too !!

[Sergey Ovchinnikov @sokrypton]

@SluskyLab Also all the folks involved in high throughput DNA sequencing, sequence databases, sequence alignment and sequence search... 🙏

[Elisa Granato @Prokaryota]

In the year of our lord 2024, how is this still a thing?! @NaturePortfolio

[Itai Yanai @ItaiYanai]

Doing good science is 90% finding a science buddy to constantly talk to about the project.