@sentausa

Bioinformatician, microbial genomics, high-throughput sequencing data analysis. Also on https://xitter.cf/t.co/dSdObksWQH

 Lyon, France
Joined November 2008
  • Tweets7K
  • Following365
  • Followers473
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Erwin Sentausa retweeted
𝕐@nomad421Oct 24
Mapping PacBio and ONT long reads to the transcriptome 26-83x faster than minimap2, in ~2.1G of memory with similar accuracy (no spliced read mapping yet tho)! crates.io/crates/spearfish-c… Details to come, but there are some docs: combine-lab.github.io/spearf… Oarfish support incoming.
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Armin Töpfer@XLROct 22
Bioinformatics is fast again! 🚀 I might have just set a record: 1 min 46 sec to analyze a 30x @PacBio HiFi human genome (90 GB), from reads to SNVs, indels and structural variants. On a single server with one GPU. That's an estimated 26 cents in the cloud.🧵
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Oxford Nanopore
@nanoporeOct 21
There's more to a repeat than length. This preprint introduces Mahi-mahi, a tandem repeat genotyper for nanopore sequencing data that reports repeat length, motif composition, interruptions and methylation from the same sequencing data. medrxiv.org/content/10.64898… Research Use Only
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Structural variant detection across sequencing technologies nature.com/articles/s41587-0…
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Atoosa Kasirzadeh
@Dr_AtoosaOct 5
🚨 Our first peer-reviewed paper on the challenges and opportunities of automating science with AI is now available at the Proceedings of the National Academy of Sciences. Read the full paper here: pnas.org/doi/epdf/10.1073/pn…
Atoosa Kasirzadeh
@Dr_AtoosaJan 27
2026 is the year of AI Scientists, among many other things. At Carnegie Mellon University, we‘re conducting some exciting research on the performance and safety of AI scientists. Our first paper “The more you automate, the less you see: hidden pitfalls of AI scientist systems” is revised and available for reading. Our work has been coverred by undark too; links to the paper and coverage here: arxiv.org/pdf/2509.08713? undark.org/2026/01/26/ai-sci…
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Erwin Sentausa retweeted
Zane Koch
@zanehkochSep 18
Science – debatably the #1 journal in the world – published a paper on a "virtual biotech" AI system this week but the authors never even test if it works well! all the evidence for its performance is 3 anecdotes the paper has no benchmark scores, no baselines, no replicates
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Erwin Sentausa retweeted
James Zou@james_y_zouSep 17
Super excited that #VirtualBiotech is published in @ScienceMagazine today! Tens of thousands of AI scientist agents work together across drug discovery + development, from target discovery to clinical trial design. Our blueprint for agentic R&D 🧵
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Long-read #sequencing is transforming our understanding of the human #genome by revealing complex genetic variations often missed by traditional methods. This #Primer explores the computational techniques enabling these insights. nature.com/articles/s43586-0…

Bioinformatics for human long-read whole-genome sequencing

Nature Reviews Methods Primers - Long-read sequencing facilitates observation of contiguous DNA molecules, providing access to variants previously ignored. In this Primer, Zheng et al. discuss the...

nature.com
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Erwin Sentausa retweeted
Bacterial Genomics@BactGenRSSAug 27
A new core-genome MLST approach for Chlamydia trachomatis genomic surveillance and research nature.com/articles/s41467-0…

A new core-genome MLST approach for Chlamydia trachomatis genomic surveillance and research

Nature Communications - The use of whole-genome sequencing for classification and surveillance of the pathogen Chlamydia trachomatis is limited due to the lack of standardized typing frameworks....

nature.com
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Erwin Sentausa retweeted
Cell Genomics@CellGenomicsAug 13
Automatic generation of model sequences for complex regions in assembly graphs with TTT dlvr.it/TV0Nv5

Automatic generation of model sequences for complex regions in assembly graphs with TTT

Antipov et al. present a tool that automates gap closure in complex genomic regions. This method replaces error-prone, labor-intensive manual curation with heuristic optimization of objective quality...

cell.com
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Erwin Sentausa retweeted
Eric Topol
@EricTopolAug 4
An AI biologist augmented discovery of disease mechanisms and targets for drug treatment. Working autonomously, trained with >24 million publications and >600TB of biomedical data @natBME nature.com/articles/s41551-0…
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Erwin Sentausa retweeted
Bacterial Genomics@BactGenRSSAug 5
Trimeric autotransporter adhesins driving chain-like adhesion diversify surface colonization strategies in Shiga toxin-producing Escherichia coli nature.com/articles/s41467-0…

Trimeric autotransporter adhesins driving chain-like adhesion diversify surface colonization...

Nature Communications - In this study, the authors demonstrate that trimeric autotransporter adhesins drive bacterial chain-like adhesion, expanding the surface colonization strategies of Shiga...

nature.com
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Erwin Sentausa retweeted
Luigi Sigillo@luigi_sigilloJul 31
🧬 Introducing 𝐄𝐌𝐁𝐋 𝐀𝐈 𝐋𝐈𝐁𝐑𝐀𝐑𝐈𝐀𝐍. A knowledge layer for life-science AI agents. Natural-language question in. Evidence snippet out. No vector database. No separate literature index. Always up to date. Open source ↓
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Manuel Corpas@manuelcorpasJul 21
1/ Out today in Cell Genomics: "Agentic genomics: From pipeline automation to autonomous validation." With @HeinnerGuio and @SFatumo . For 20 years the bottleneck in genomics was writing the code. That is going away.
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nature
@NatureAug 3
Nature research paper: A global view of human centromere variation and evolution go.nature.com/4bnIAb7

A global view of human centromere variation and evolution

Nature - Complete sequencing of more than 2,000 centromeres from diverse humans reveals structures and elevated mutation rates that shape the evolution of these critically important regions.

nature.com
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Erwin Sentausa retweeted
Matthias Mann Lab@labs_mannJul 28
Can AI take proteomics to a virtual cell? Our new perspective maps the path — from better peptide/protein ID to spatial & perturbation proteomics to AI Virtual Cells — and calls for an AI-friendly data ecosystem to get there. @guomics and Zhang lab. nature.com/articles/s41592-0…

AI proteomics: from protein identification to virtual cells

Nature Methods - This Perspective highlights key research areas within mass spectrometry-based proteomics where AI is poised to drive significant advances.

nature.com
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Erwin Sentausa retweeted
Bacterial Genomics@BactGenRSSJul 24
A prehistoric East-Asian Yersinia pestis genome and a ~5.3 ka trans-Eurasian expansion of plague nature.com/articles/s41467-0…

A prehistoric East-Asian Yersinia pestis genome and a ~5.3 ka trans-Eurasian expansion of plague

Nature Communications - Plague, caused by the pathogen Yersinia pestis, has affected human societies for millennia. Here, the authors screened 1,400 ancient human remains from eastern Eurasia and...

nature.com
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Erwin Sentausa retweeted
Ming "Tommy" Tang@tangming2005Jun 16
Someone asks me every other week if AI is going to replace bioinformaticians. A new npj Digital Medicine paper finally said what I have been telling them for two years.
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Our new genome annotation method relies almost entirely on transcriptome and alignment evidence, and as a result outperforms pretty much all other de novo pipelines. Paper just out, led by @AlekseyZimin5: rdcu.be/frSOg
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Erwin Sentausa retweeted
James Zou@james_y_zouJun 29
Excited to introduce Paperclip Chat!🖇️ Now you can use #Paperclip directly in your browser for deep literature synthesis for free ⚡️ Each claim is grounded with inline citations ⚡️ Upload your own PDFs. They're automatically integrated into Paperclip's virtual filesystem
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