Manolis Kellis

Kellis Lab is hiring! New grants in #Alzheimers #Schizophrenia #Cancer #EHR #SingleCell #Genome #Epigenome #Transcription #Disease integration. Computational & experimental positions, profiling and circuitry dissection. Join us! @MIT_CSAIL @BroadInstitute compbio.mit.edu/positions.html

I’m happy to share our latest preprint, sc4D, led by the incredible Ishir Rao @ishirraov! We developed a new #computational approach to model #spatiotemporal #transcriptional #dynamics in disease progression 🧬.

Excited to share our latest preprint by Alexis Yang and Gary Lee, in collab with the @jberchuck lab: biorxiv.org/content/10.110…. We found that transcription of enhancers (a mark of activation) causes distinct fragmentation patterns in #cfDNA.

@ZeTristanShi Wonderful meeting you ZeChuan! :-)

Finally coming up for air from paper revisions & others 😅 Looking back on #ASHG25 — such an inspiring week! Learned a ton about foundation models and other ML models reshaping genomics, plus got to chat with @manoliskellis and his team. Back to work 🧬

So proud of #RileyMangan and #NikithaThoduguli presenting platform talks at #ASHG25 today on #SingleCell phenotypes for #Alzheimers, and #DeepLearning #Evolution of human cis-regulatory elements. Spread the word! @MIT @BroadInstitute @HarvardMed

MIT Course announcement: Machine Learning for Computational Biology #MLCB25 Fall'24 Lecture Videos: tinyurl.com/MLCBlectures Fall'24 Lecture Notes: tinyurl.com/MLCB24notes (a) Genomes: Statistical genomics, gene regulation, genome language models, chromatin structure, 3D genome topology, epigenomics, regulatory networks. (b) Proteins: Protein language models, structure and folding, protein design, cryo-EM, AlphaFold2, transformers, multimodal joint representation learning. (c) Therapeutics: Chemical landscapes, small-molecule representation, docking, structure-function embeddings, agentic drug discovery, disease circuitry, and target identification. (d) Patients: Electronic health records, medical genomics, genetic variation, comparative genomics, evolutionary evidence, patient latent representation, AI-driven systems biology. Foundations and frontiers of computational biology, combining theory with practice. Generative AI, foundation models, machine learning, algorithm design, influential problems and techniques, analysis of large-scale biological datasets, applications to human disease and drug discovery.  First Lecture: Thu Sept 4 at 1pm in 32-144 With: Prof. Manolis Kellis @manoliskellis, Prof. Eric Alm @ejalm, TAs: Ananth Shyamal, Shitong Luo @luost26 Course website: compbio.mit.edu/mlcb @MIT @MITEECS @MITdeptofBE @MITCSBPhD @MIT_CSAIL @Harvard @HarvardMed @BroadInstitute

Mature and migratory dendritic cells promote immune infiltration and response to anti-PD-1 checkpoint blockade in metastatic melanoma @NatureComms @gmboland @manoliskellis nature.com/articles/s4146…

I could never imagine combining deep conversations on #AI & #longevity with the beauty of my beloved Andros… until the AI Longevity Salon, hosted by @manoliskellis - where science met philosophy & ideas on longevity flowed. Thanks, Manolis, for the photos & the inspiring event.

Excellent talk by @manoliskellis at Athens College on AI and navigating complex data with Mantis. home.withmantis.com

If you are at ICML2025, welcome to attend our workshop "Multi-modal Foundation Models and Large Language Models for Life Sciences" tomorrow (Jul 19 Saturday). The workshop features a stellar lineup of invited speakers, including Valentina Boeva @val_boeva, Manolis Kellis @manoliskellis , Jure Leskovec @jure , Jian Ma @jmuiuc, Bahareh Tolooshams @BTolooshams, Mengdi Wang @MengdiWang10 , Eric Xing @ericxing , Marinka Zitnik @marinkazitnik , 70 accepted papers, and four contributed talks. Huge thanks to my co-organizers: James Zou @james_y_zou , Le Song @dasongle , Aidong Zhang, Ruiyi Zhang, Danielle Grotjahn @nani_grotjahn, Linda Awdishu @LAwdishu, Eran Segal @segal_eran , and Wei Wang @WeiWang1973 .

Greek friends, join us next Sunday July 6 in @Athens, as we hack the Future of #AI in the Cradle of Western Civilization, at the #EugenidesFoundation. After the success of our last hack at MIT, we're partnering with SundAI Club again to bring cutting-edge technologies to the Hacker and Builder communities of the world. Register here: lu.ma/hwxuxliq (1) WhatIsMantis: Imagine peeking into the mind of an AI like ChatGPT, and #visualizing how it organizes ideas, thoughts, documents, proteins, drugs. Imagine watching them come to life as you speak with the AI, revealing meaningful #constellations of relevant information in a cognitive landscape of information. Now, imagine a full cognitive #workbench that allows you to manipulate these clusters directly, powered by visual tools, next-gen search, auto-macros, agentic workflows, and real-world actions. Lastly, imagine working with your team and #collaborators on shared workbench, with multiple interlinked cognitive floors, co-browsing, taking joint actions, partitioning tasks, visualizing trends, detecting outliers, and sharing discovery journeys in a predictive, learning, adapting system, fully integrated within your daily workflows. See Mantis Demos: tinyurl.com/MantisDemos (2) On July 6, you can bring this vision to reality, by using our Mantis AI platform to create your own applications and solutions in any vertical, and turn unstructured data into structured insights, semantic graphs, hierarchical ontological views, custom vertical-tuned tools, and agentic workflows bringing data to life and revealing systematic insights. We'll start with breakfast and intros, brainstorming and team formation, dataset gathering and project refinement, and tool creation across agents, journeys, workflows, and interactive coding notebooks, all in one day in Sundai Club fashion! See our last hacks here: sundai.club/projects (search: Mantis) (3) We’ll have applications in education, law, government, startups, investment, cultural heritage, tourism, news, politics, media, jobs, policy, customers, reddit, YouTube, shopping, Linkeode, healthcare, drug discovery, or anything that you are passionate about. You can work alone or in groups, bring your own team or make new friends, bring your own data, work with our sample datasets, or scrape away, with many members of our team supporting in person and remotely. (4) Links: - Create a Mantis account here: home.withmantis.com/inquire - Use Mantis here: alpha.withmantis.com - Join the Mantis team here: tinyurl.com/MantisOnboardi… With Serge Vasylechko, Konstantina Yaneva, Christina Koutsoumpa, PhD, Vassilis Papakonstantinou, Alexios Ntavlouros, Nicolas Pigadas, Minas Megalokonomos, Pascal Passigan, Jophy Ye, and many members of the Sundai and Mantis AI teams joining remotely! All participants to the Hackathon will get a free ticket to the #UniversalAI launch event on Tuesday July 8, with Dimitris Bertsimas, Theodoros Evgeniou, and more. uaisummit.mit.edu

So excited to speak on #AI powered #DrugDiscovery at 10am this morning, at the @MIT Club of Boston @MITboston BioSummit on AI in HealthCare and Biotech. *Live now on Zoom*: lnkd.in/eqb88mbE Already 140 attendees and growing, please join us! @MIT_alumni @MITBiology @MITEECS @MITBiotechGroup @csail_alliances @MIT_CSAIL @DrAnneCarpenter @broadinstitute @FlagshipPioneer @harvardmed

If you love #Hacking and building the future of #AI, join us next Sunday May 18 for a joint #Hackathon with @Sundai_club (Boston), and Æthos (Berlin). You can be one of the first to build on our #Mantis Cognitive Cartography Platform for Human-driven AI-powered Visual Data Science, pre-released for the first time. Boston sign-up: partiful.com/e/Rv9XUxKjkwdq… Berlin sign-up: lu.ma/event/manage/e… Super excited to see what everyone builds!! Learn more: tinyurl.com/MantisDemos Join our team: tinyurl.com/MantisOnboardi… with Serge Vasylechko, Gabriela Torres Vives, Konstantina Yaneva, Chris Hahn, Sam Rowe, Isabella Douzoglou, Christina Koutsoumpa, Yiyang Lu #HackersUnite

Please join us for an @MITBiotechGroup and @MITEECS and @IEEEorg @TheACMG joint mixer tonight, at the interface of #ComputerScience and #Biology. Mixer from 6pm-7pm, and panel conversation from 7pm-8pm, in the @MIT #StataCenter student street, room 32-144. Excited to many of you tonight! RSVP here: tinyurl.com/MBGmixer @MITBiology @MIT_CSAIL @MIT_SCC @MITCSBPhD

Join us to celebrate #Easter in the #Greek tradition at the heart of @MIT today. Roasting 5 whole lambs on a spit, grilling juicy pork souvlaki, Greek specialties including mousaka, pastitsio, tzatziki, horiatiki greek salad, galaktompoureko (google it!), baklava, and of course Traditional Greek Line Dancing and more! More info here: mit.universitytickets.com/w/event.aspx?i… Photos from previous years: Easter 2023: photos.app.goo.gl/J8KhZ7T83wuihq… Easter 2022: photos.app.goo.gl/zAake6jQwV7m2f… Easter 2019: photos.app.goo.gl/FvPP1fYsxHSAgM… Easter 2017: goo.gl/photos/CnCnmRz… Weather seems *perfect*, and the lambs should be ready by 12:45am, so come on time and enjoy!!

.@MIT_CSAIL Prof. @manoliskellis is reimagining healthcare with AI: from one-size-fits-all drugs to precision, modular treatments tailored to each patient’s biology. His lab is mapping disease at the molecular level to revolutionize drug discovery. More: bit.ly/43S6clm

Confirmed keynote speakers for the Greeks 🇬🇷 in #AI 2025 Symposium in Athens, Greece 🤗

@jebibault @FranceinBoston @villa_albertine Looking forward to it, see you there! :-)