ASFV, AIV, PRRSV genomics; nanopore sequencing Information System developer @ Armont Business Solutions and Asst. Professor @ UP Los Baños, Philippines;

Philippines
Joined July 2010
We are the @nanopore User Group Philippines! Established 27 June 2023 Los Baños, Laguna, Philippines
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Andrew Montecillo retweeted
🧬 Big news: myloasm, a metagenome assembler written entirely in Rust, landed in Nature Biotechnology. It untangles closely related strains in noisy long-read data better than anything before it. Rust doing science. 🔗 github.com/bluenote-1577/myl…
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Andrew Montecillo retweeted
Whole-genome variant calling... on your laptop... in under 100MB of RAM. Rosalind (Rust, obviously) went viral on HN this year for doing exactly that, with byte-for-byte reproducible outputs and zero cloud upload. Your genome, your machine. 💻🧬 🔗 github.com/logannye/rosalind
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Andrew Montecillo retweeted
#MicrobiologyMonday: Bunsen burners are used to reduce airborne contamination. Data in #JournalSpectrum suggest the practice is not evidence-based and, except in some cases, Bunsen burners can be removed from practice w/o compromising research integrity. asm.social/33D
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Andrew Montecillo retweeted
Aloha! 🌺Introducing Ornith-1.5, a family of open-source LLMs spanning 9B Dense, 35B MoE, and 397B MoE, trained with self-improving strategies. It achieves state-of-the-art performance among open-source models of comparable size and delivers performance comparable to Claude Opus 4.8 across reasoning, agentic, and coding tasks: ✅Terminal-Bench 2.1 (86.1) ✅SWE-Bench (86 on verified, 65.1 on pro, 79.6 on Multilingual) ✅DeepSWE (56) ✅HLE (44.6) ✅ClawEval (81.4) ✅Tool Decathlon (71.2) Ornith-1.5 takes a major step toward training foundation models through end-to-end self-improvement, extending the self-scaffolding strategies introduced in Ornith-1.0 into a more complete self-improvement loop: the model proposes new tasks, generates task-specific scaffolds, and produces solution rollouts for reinforcement learning, continuously creating new learning experiences from which it can improve. All models, along with their quantized versions (FP8, GGUF, MLX, and NVFP4), have been released under the MIT License, enabling unrestricted commercial and research use. 📘Tech Blog: ornith.ai/ornith_1_5.html 🤗Huggingface: huggingface.co/collections/o…
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Andrew Montecillo retweeted
Biology has no shortage of data. The challenge is to organize it well enough that scientists—and machines—can learn from it. Our latest preprint presents AllTheBacteria: an open, community-built platform that transforms 2.44 million public bacterial and archaeal genomes into a uniformly processed, searchable, and AI-ready resource. To demonstrate what becomes possible at this scale, we used the platform to discover new peptide antibiotics. One candidate, ATB20, reduced Acinetobacter baumannii burden in a murine skin-abscess model, with efficacy comparable to polymyxin B. More broadly, this work illustrates how open, standardized biological data can help us use machines to understand and engineer biology—and accelerate the discovery of new potential solutions for human health. Deeply grateful to the remarkable international team behind this work: Martin Hunt, Daniel Anderson, Maria Luiza Andreani, Josefin Blom, Michael B. Hall, Samuel T. Horsfield, Hyun-Su Lee, Leandro Lima, Neil MacAlasdair, William Matlock, Vignesh Ramnath, Vishnu Raghuram, Matthew J. Russell, Liam P. Shaw, Gerry Tonkin-Hill, Jackie Toussaint, Fangping Wan, Laura M. Carroll, Matthew A. Croxen, @mdt_torres, @happy_khan, @GB13Faithless, @fionabrinkman, @AndresFloto, @yekwah, @bfjia, @Jake_A_Lacey, @sudaraka_m, @Ahmed_Microbes, @rpetit3, @theosanderson, @TimoSaratto, @oschwengers1, @torstenseemann, @shenwei356, @nrt_thomson, @thanhleviet, @vWachsmann, @aaron_weimann, @WheatleyRM, @wiatrak_maciej, @ouli_xie, @johnlees6, and @ZaminIqbal. With colleagues across @sangerinstitute, @emblebi, @NDMOxford, @Penn, @TheQuadram, @TheCGPS, Universidade Estadual de Campinas, @Ucmr_sweden, @BHIresearch, @mbbsfu, @WCHRIUofA, @LKSIoV, @CC4AIM, @HLRI_Cambridge, @AlfredMonash_ID, @CentreImpactAMR, @UniNeuchatel, @TheDohertyInst, @PeterMacCC, @UniOslo, @MilnerCentre, @LSHTM, @jlugiessen, @BristolBiochem, @Cambridge_SBS, and Theiagen Genomics. biorxiv.org/content/10.1101/…
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A surprising finding: nearly all bacterial contamination in your grocery store's fresh or frozen chicken originates in a tiny number of breeders, not at the massive chicken breeding farms. We might be able to eliminate these contaminants cheaply pnas.org/doi/10.1073/pnas.25…
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Science twitter, do your thing: Shotgun metagenomics via SISPA amplicon sequencing using ONT platform (PROM flowcell, latest Dorado sup model) with median read length of 400 bp. Which assemblers to use?
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Andrew Montecillo retweeted
Yann LeCun just exposed AI’s fundamental flaw. We’re celebrating systems that can’t do what insects do effortlessly. LeCun: “The biggest difficulty is not to get fooled into thinking that a computer system is intelligent simply because it can manipulate language.” Language feels like intelligence because we experience it as the highest form of human thought. So when a machine produces fluent, articulate, convincing text, the instinct is to conclude it understands. It doesn’t. LeCun: “It turns out the real world is much, much more complicated.” Language is actually the easy part. A sequence of discrete symbols with a finite number of possibilities. Predicting the next word is a tractable mathematical problem. Impressive at scale. Not understanding. Pattern matching in symbol space. The real world is something else entirely. A high-dimensional, continuous, noisy signal that changes every millisecond in ways no text corpus can capture. Physical reality doesn’t come in tokens. LeCun: “Which your house cat is perfectly able to deal with. But not computers yet.” This is the Moravec paradox. The things that feel hard to humans: writing essays, solving equations, passing bar exams. Computationally straightforward. The things that feel trivially easy: walking across a room, catching a falling object, folding a shirt. Extraordinarily difficult for machines. Your house cat navigates a complex three-dimensional physical environment in real time. Predicts trajectories. Adjusts to surprises. Understands cause and effect through direct interaction with the world. The most powerful AI systems ever built cannot do what your cat does before breakfast. That’s not a minor gap. That’s the entire frontier. Language is the easy problem that looks hard to humans. The physical world is the hard problem that looks easy because evolution solved it billions of years ago. We’re pouring hundreds of billions into making language models marginally better at the simple problem. The actual intelligence problem remains unsolved. LeCun has spent fifteen years on this. Not making chatbots more fluent. Giving machines the ability to understand, predict, and interact with physical reality the way animals do instinctively. The benchmark that matters isn’t passing a bar exam. It’s folding a shirt. Loading a dishwasher. Navigating an unfamiliar room without a map. We built systems that can write your dissertation before we built systems that can tie your shoes. That’s where AI actually is. Everything else is autocomplete at scale.
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Andrew Montecillo retweeted
Tools and approaches to study the human gut virome: from the bench to bioinformatics journals.asm.org/doi/full/10…
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Andrew Montecillo retweeted
HiMBar: A High-Fidelity Metagenomic Barcoding Approach for Transkingdom Species Detection and Interaction Analysis in Aquatic Ecosystems onlinelibrary.wiley.com/doi/…
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Andrew Montecillo retweeted
We built an ultra-fast genomics viewer for the browser. Before YouTube, sharing videos online was painful. Files were too large to email, too large to host, formats were not standardized, and each video existed in isolation instead of as part of a wider database. This is the situation we are in with omics and other medical data. Current viewers are either slow browser tools with few features, or desktop applications requiring large file downloads before use. We want to make complex biomedical data more accessible over the internet, and critical to that is a fast, secure genomics viewer in the browser. Today we're happy to show off our viewer. It performs like a desktop application, doesn't require large file transfers, and enables secure collaboration. We don't have open access yet, but if you'd like to give it a spin, shoot me a DM hox.bio/blog/genomics-viewer
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Andrew Montecillo retweeted
Reducing haystacks to needles - ViralClust: A Nextflow pipeline to cluster viral sequences | bioRxiv biorxiv.org/content/10.64898…
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Andrew Montecillo retweeted
I think the coolest looking structure/sequence viewer for protein design right now is the one by BioGeometry, good UI/UX, great visuals Cooking one of my own up right now, we'll see how it turns out
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Andrew Montecillo retweeted
We @abscibio are excited to share Origin-1, our platform for de novo antibody design! We select "zero-prior" epitopes without guidance from or the availability of solved protein-protein complex structures and, using fewer than 100 designs per target, achieve success against four targets: COL6A3, AZGP1, CHI3L2, and IL36RA. We validate binding, developability, and function via multiple orthogonal assays and confirm atomic accuracy with Cryo-EM for two targets. We share detailed methods, including on the models underlying Origin-1, and release our data as a resource for the community. 📄 Read the preprint: absci.com/wp-content/uploads… 📊 Access our data: github.com/AbSciBio/origin-1
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Visualizing pairwise genome comparisons? No need to run BLAST separately anymore! 🧬 ​#gbdraw has implemented #LOSAT, a WASM-powered Rust reimplementation of BLASTN/TBLASTX. ​✅ No local installation ✅ No data transfer (Serverless) ​Try it here: gbdraw.app/
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