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.ht…

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

Immensely proud to share our four papers on #SingleCell dissection of #Alzheimers Disease coming out in @CellCellPress today, reporting 2.3M #scRNA profiles and 850k #scATAC profiles across 427 post-mortem human brain samples from AD and non-AD donors in a wonderful #interdisciplinary collaboration with @DrLiHueiTsai between @MIT @MIT_Picower @MIT_CSAIL @BroadInstitute @RushUniversity Paper 1: scRNA + vulnerability + resilience cell.com/cell/fulltext/S0092… Paper 2: scATAC + GWAS + Epigenome Erosion cell.com/cell/fulltext/S0092… Paper 3: Microglia States + reprogramming cell.com/cell/fulltext/S0092… Paper 4: DNA damage + gene fusions cell.com/cell/fulltext/S0092… MIT News: news.mit.edu/2023/decoding-c… Issue: cell.com/cell/current News & Views: cell.com/cell/fulltext/S0092…

This week in @Nature we present our #SingleCell dissection of #ApoE4, the strongest genetic variant for #Alzheimers. ApoE4 impairs #cholesterol #transport, leading to #oligodendrocyte ER accumulation, decreased #myelination. Restoring transport restores mouse cognition. #Hope #AD

Excited to share our #MultiRegion #SingleCell dissection of #Alzheimers out in @Nature today studying #Reelin in #RegionSpecific #NeuronalVulnerability, #CholineMetabolism and #PolyAmineBiosynthesis in #CognitiveResilience, #Astrocyte diversity, #Thalamus-specific #Interneurons, #scDemon for #Module analysis, and so much more. Paper: nature.com/articles/s41586-0… News: picower.mit.edu/news/study-a… Website/Data: compbio.mit.edu/ad_multiregi… Interactive website: compbio2.mit.edu/ad_multireg… Cell Browser: ad-multi-region.cells.ucsc.e… Code: github.com/cboix/admultiregi… scDemon module analysis: github.com/KellisLab/scdemon with: @Carles_Boix, @MathysHansruedi, @Leyla_Aakay, @DrLiHueiTsai, #DavidBennett, @RudyTanzi, @__ben_james__, @_JoseDavila, #KikiGalani, @NeilBBand, @NIHAging, #CureAlz and so many more amazing contributors. Truly grateful for an amazing team and collaboration #OpenAccess #OpenScience #NeuroDegeneration

Today was my last lecture for @MIT #ComputationalBiology: #Genomes, #Networks, #Evolution, #Health. I recorded each and immediately posted online here: piped.video/playlist?list=PL… Please do share, and let me know which topics need more explanations, clarifications, and corrections!

To the colleagues and friends who find our paper overwhelming, and instead prefer to write and read more manageable papers with more focused messages: I respect your perspective and your approach to science greatly, and find it invaluable, of course. Both broad and focused papers are needed in science, and we can't all write exactly the same type of paper, and we can't all be the same. Some papers/authors lay the 'landscape', other papers/authors dive deeply into the 'portraits' of specific genes and pathways. Instead of simply dismissing our work as "TL;DR" and moving on, I encourage you to consider the value of not just releasing data, but also guiding the reader in how the data can be studied, as supporting points for detailed papers that dive into specific insights and facets. As a genomicist, I have sought to contribute resource papers to the community across different fields (epigenomics, comparative genomics, single-cell, GWAS interpretation). Thousands of scientists have found our papers valuable through the years, and I already see the same excitement for this paper and resource from hundreds of scientists that responded overwhelmingly positively both to the resource and to the specific insights and hypotheses raised, both publicly and privately. Following up on each of these hypotheses will take years and dedicated PhD and postdoc projects (and ultimately preclinical and therapeutic projects in industry), which are simply impossible tasks in the first landscape paper releasing the resource. If one agrees that there is value in generating such massive datasets (and I'm happy to have this debate as well), I see three paths for publication: (a) Simply upload the massive dataset on a website and let others figure it out (with appropriate privacy protections); or (b) Wait 5-10 years for all the pathways and discoveries to be fully fleshed out in one giant paper or a series of papers as a 'package'; or (c) Somewhere in the middle, namely releasing the data, providing illustrations of the types of analyses that can be carried out and the insights and tantalizing hypotheses they reveal, and carrying out initial experimental validations to provide validation support for some of our highlighted findings, with the understanding that fully pursuing any one of these insights will take many years and dedicated efforts by 'portrait' scientists. With approach (c), which we tried to take, the large number of figures and panels in such 'landscape' papers seeks to guide the reader for how to explore the complexity of the dataset and the questions that can be answered. Each of these figures will take time to study, understand, reflect on, improve on, and hopefully each and all together will play a role in seeding ideas and insights, and pushing the field forward. It is normal for such massive papers and resources to take days, weeks, months, and sometimes years to fully understand, and to fully extract maximum value from. It was a herculean task by the reviewers and editors, as it was of course for the authors, to go through every figure, every panel, and every result. Of course there will be some mistakes that slipped through that process, and these will be corrected and improved up, with better methods, newer pipelines, and fresh perspectives, in science's self-correcting entreprise. We will learn from our mistakes, and from mistakes of others, and our next papers will hopefully be better, clearer, and more useful, though they will never be perfect, but hopefully sufficiently good to let others build on them and surpass them. For those readers genuinely overwhelmed by the number of figures and panels in such papers, think of them as a good book with many chapters and many pages, not a YouTube short. Each paragraph, parenthesis, panel, supplementary figure, can hide potential hints and secrets that the authors themselves may have missed, and tools like the ChatGPT Consensus app can help elucidate, and dive deeply into specific hypotheses for hours of exploration. Ultimately, the best part of the paper begins *after* its publication, as countless students, postdocs, and group leaders dive into the findings, and weave their own stories from the threads each paper puts out. So happy exploring and weaving, and may this paper generate more questions and hypotheses that we could have even imagined. With love to all -Manolis

The field of #ComputationalBiology has changed dramatically in the last few years with #GenerativeAI. I'm excited to be recording my lectures again this year, and to be teaching with the awesome @EjAlm. You can find the first lecture here: piped.video/1zZSPeKGRzw and more will be coming in the playlist below. Fall 2024: piped.video/playlist?list=PL… Spring 2021: piped.video/watch?v=0jWOZoTs… Fall 2020: piped.video/watch?v=CTPs5HEL… #CompBio #DeepLearning #MachineLearning #Genomics #Therapeutics #RepresenationLearning #Chemistry #ProteinFolding #ClinicalRecords #SingleCell

The first six lectures of #DeepLearning for #Genomics and #LifeSciences are posted on @YouTube here: piped.video/playlist?list=PL… covering #MachineLearning #CNNs #RNNs #GNNs #RepresentationLearning #InterpretableML #Convolution Linking to them individually in the thread below 1/n

Our #EpiMap paper is now @Nature: systematic dissection of #DiseaseCircuitry, including predicted driver variants, enhancers, regulators, target genes, and relevant tissues/cell types across 30,000 genetic loci, 540 traits, 833 tissues rdcu.be/ceIb4 #Epigenomics #GWAS

Such an honor to be back on @LexFridman to talk about #humanity, #AI, #intelligence, #ChatGPT, #DeepLearning, #DrugDiscovery, #Genomics and the #FutureOfWork. Lex is an amazing human being, curious, driven, smart, humble, kind, and unapologetically open. Thank you Lex for the many conversations, your thought-provoking questions, and your love of humanity. I always learn so much from you, your guests, and your insights 🤖🧠🫀🧬

"The only thing more full than the auditorium tonight is @ManolisKellis poster" @LB_Barreiro intro at #BoG22... Ahem... you be the judge. Poster #135, come say hi! Full res here: dropbox.com/s/1zbjwcah7qmt5d… #Alzheimers #SingleCell

Our #SingleCell #Alzheimers dissection of 80,000 cells across 48 human brains with @DrLiHueiTsai is now online news.mit.edu/2019/gene-map-a… @Nature @MIT_Picower @MIT_CSAIL @MIT @BroadInstitute @ScienceMIT @MITbrainandcog @HarvardMed @MITEngineering @MITEECS nature.com/articles/s41586-0…

Excited and proud to share our #SingleCell dissection of #ALS and #FTLD out in #Cell this week, across 620,000 cells, 44 cell types, 73 donors, and two brain regions. Although ALS affects #movement vs. FTLD #cognition, the two are nearly identical in the cell types, genes, and pathways they affect, both in #familial (monogenic) and in #sporadic (polygenic) cases, providing hope and candidate targets for common #therapeutic programs, implicating #LongRange-projecting neurons, and #cilia genes and pathways, necessary for their growth, but also #vascular changes and blood-brain-barrier function and integrity. News: news.mit.edu/2024/als-ftld-s… Paper: cell.com/cell/abstract/S0092… Preprint: doi.org/10.1101/2021.07.07.4… Data: synapse.org/#!Synapse:syn511… #NeuroDegeneration #ADRD #Alzheimers #FTD #FrontoTemporalDementia #LouGehrigsDisease #MyriamHeiman #SebastianPineda #VeroniqueBelzil #LiveLikeLou @iamalsorg @bsw5020 @alsadvocacy @ProjectALSorg #MotorCortex #BetzCells #VENs #C9orf72 #TDP43 #NeuroDegen #MCx @MTPA_US @NIH @NIHAging @GerstnerFdn @PackardFdn

Our #scMetab paper is out today #SingleCell dissection of #Obesity-#Exercise axis in #Adipose-#Muscle metabolic tissues @Cell_Metabolism #MultiTissue #CellCommunication #Diet #healthy @MIT News: news.mit.edu/2022/genes-path… Paper: sciencedirect.com/science/ar… Data: scmetab.mit.edu

Excited to share our #SingleCell dissection of human #vasculature with #MyriamHeiman across 17 cell subtypes, human-specific #zonation, vasculature-coupled glia/neurons, and #Huntington's-associated #immune activation and #BBB integrity breakdown. #scBBB biorxiv.org/content/10.1101/…

Proud to share our #eGTEx multi-tissue dissection of #enhancer H3K27ac across 387 brain, muscle, heart, and lung samples from #GTEx in @NatureGenet #eQTLs #haQTLs #SexDiffs #Epigenomics #GWAS #linking Paper: nature.com/articles/s41588-0… (H3K27ac, today) News: csail.mit.edu/news/unlocking… m6A paper: go.nature.com/3qGg3VI (2021) @MIT @MIT_CSAIL @BroadInstitute @MITEECS @MIT_SCC @harvard @harvardmed @GTExPortal

Our #SingleCell dissection of #Schizophrenia genes/pathways, a new #TranscriptionalResilience cell type, target genes at #GWAS loci, and upstream #MasterRegulators is out @medRxivPreprint #PsychENCODE #BradRuzicka @Mohammadi_PhD #JoseDavila @NIMHgov medrxiv.org/content/10.1101/…

Excited to share our #SingleCell dissection of #Schizophrenia, out in @ScienceMagazine today, reporting 470k cells in 27 cell types across 140 individuals from 2 cohorts, revealing key insights on #ExcitatoryNeurons, #NeuroDevelopment, #Synapses, #1Cmetabolism, #Genetics, #Subtyping, #NetworkConvergence, #TFs, #DEGs, #GWAS, #RareVariants, and #DiseaseMechanism, with @Brad_Ruzicka @LabRoussos @ShahinMohammadi @_josedavila #PsychENCODE2 Paper: science.org/doi/10.1126/scie… Collection: science.org/collections/psyc… Science tweet: nitter.app/ScienceMagazine/… Big thanks to @NIH, @NIMHgov, #PsychENCODE

Excited to share our #SingleCell #MultiTissue Dissection of #Obesity-#Exercise axis in #Adipose #Muscle tissues biorxiv.org/content/10.1101/… Central roles of #StemCells #Thermogenesis #ExtraCellularMatrix #Circadian #Tcells #CellCommunication #scMetab #Metabolism #scWAT #vWAT #SkM

Excited to share our #SingleCell dissection of #Alzheimers brain #vasculature changes across 6 brain regions with @DrLiHueiTsai. AD- & ApoE4-associated DEGs, upstream regulators & modules, cell-cell communication changes and links to #GWAS variants biorxiv.org/content/10.1101/… #ROSMAP

Excited to share our #SingleCell dissection of #LivingHeart and #HeartFailure biorxiv.org/content/10.1101/… Led by #SuviLinnaKuosmanen @EloiSchmauch w/ #KikiGalani #TuomasKiviniemi #GuillermoGarciaCardena #MinnaKaikkonen @Calum_OG #OpenHeartSurgery #Ischemic #Cardiac #CAD #scCAD #GWAS

Interested in #DeepLearning for #Genomics and the #LifeSciences? Our @MIT course starts again today. Recommend your favorite papers and topics to cover, and we *will* cover them! Watch our 2020 lectures with @DavidKGifford at mit6874.github.io/ and piped.video/playlist?list=PL…

If a critic *never* genuinely points out the slightest positive about a work or author they're constantly criticizing, it's much easier to 'see through them' and understand that their motivations might be shooting down, bullying, settling scores, belittling, self-aggrandizing, etc., instead of genuinely trying to improve someone's work, or the broader field. The piece annotated below can provide some context on possible motivations for systematic bullying by systematic bullies against their systematic targets. Perhaps the targets leaving the field is not an innocent accident, perhaps it's the very motivation and goal, as a way to advance the bully's own career. Ad-hominem attacks, even against those who stand up against the bullies, are not uncommon, leading to a high-school courtyard mentality, where piling on is the way to show allegiance to the cool kids, instead of standing up against bullying. I wish we could all see through this more clearly, including the actual victims of bullying (who often just shut down or leave the scene), supporters of the bullies (who sometimes pile on with their own insults), and silent bystanders (who perhaps don't understand the broader context and motivations). We need to talk more openly about this as a community. Self-improving science would self-improve so much faster with kindness and constructive criticisms. We should not confuse systematic bullying with constructive feedback. The approaches, motivations, and outcomes, are very very different. Take a closer look, it's unmistakable.

Excited to share our #SingleCell dissection of human #Hippocampus #EntorhinalCx #Anatomical substructures & stage-specific changes in #Alzheimers biorxiv.org/content/10.1101/… with @DrLiHueiTsai #JoseDavilaVelderrain @MathysHansruedi @Mohammadi_PhD @Brad_Ruzicka #DavidABennett #ROSMAP

My academic family surprised me with a birthday cake and celebration today. A bit of warmth and hope among all the suffering in the world. Wishing health, safety, and peace to all

High-altitude adaptation #StructuralVariants signals in #SingleMolecule @nanopore sequencing between 119 #Tibetan and 201 #HanChinese samples reveals cis/trans rewiring of #hypoxia, #energy, #lung pathways, expanding #GWAS. #SVs #InDels #SNPs #LongReads biorxiv.org/content/10.1101/…

Excited to share our #eGTEx #m6A #QTL profiling and analysis of #brain #heart #muscle #lung in @NatureGenet go.nature.com/3qGg3VI by @Xushen18 @kdyhl @ypp_lab #BenoitMolinie #RichardGregory @GTExPortal @NIH @NIH_CommonFund #GTEx #EpiTranscriptomics #m6AQTLs #eQTLs #RBPs #GWAS

End of evolution: transforming medicine through AI to reverse human disease ted.com/talks/manolis_kellis… @TEDTalks #TEDxMIT #Genomics @MIT @BroadInstitute @MIT_CSAIL @MITEECS @HarvardMed #pharma

Excited to kick off the @MIT #Bioinformatics Seminar Series at 11:30am-1pm today. Please do join us! Title: From #Genomics to #Therapeutics: #SingleCell dissection and manipulation of #DiseaseCircuitry Info: math.mit.edu/compbiosem/ Where: MIT Stata Center 32G-575 Zoom: mit.zoom.us/j/93513735220 Quite an awesome line-up, thrilled to be part of it! #Alzheimers #Obesity #Schizophrenia #ALS #Microglia #Addiction #Epigenomics #Disease #GWAS

How bullying becomes a career tool: "Bullies spring into action when their targets become too successful for their liking". "Planting false stories, publicly ridiculing, insulting, or tarnishing". Do we have mechanisms to combat this? Can kindness prevail? #StopBullying

Parm, this is such a sweet note. Truly grateful for your kindness. I'm still that immigrant kid who will not insult anyone, and will always look for the good in people, so this behavior is quite foreign and baffling to me as well. So happy that my lectures and papers have been helpful to you, and eager to meet sometime, in person or on zoom. Wishing you all the best with your many endeavors, and thank you again for your support. It means a lot! 🥰🙏🥲

Excited to co-teach "#Neurogenomics: Computational Molecular Neuroscience" this Spring at @MIT, a new 6-9 (#EECS & #BCS) course with #MyriamHeiman. More info at compbio.mit.edu/6.883 Course syllabus below. @MITEECS @MITBrainAndCog Please spread the word! #AI #CogSci #ML #MolBio

So excited to share our #SingleCell dissection of #Alzheimers brain #vasculature changes across 6 brain regions, out in @NatureNeuro today. Paper: nature.com/articles/s41593-0… News: csail.mit.edu/news/unweaving… Open Access Link: rdcu.be/ddxxX With @DrLiHueiTsai @NaSun818 @Leyla_AAkay @MhMurdock1 @RachelEvaGordon et al

Excited to share our #SingleCell dissection of #MotorCortex in #ALS and #FTLD biorxiv.org/content/10.1101/… #BetzCells #VENs #C9orf72 #TDP43 #POU3F1 #ADRD #NeuroDegen #MCx #Alzheimer with #SebastianPineda #VeroniqueBelzil #MyriamHeiman #HyeseungLee @B_Fitzwalter @Mohammadi_PhD @MTPA_US

Happy 200 years #Greece! @MFABoston dons its blue & white stripes for your #bicentennial. So proud to live in the #AthensOfAmerica #Boston #Greece200years #Greece1821 #Greece2021 #Ελλαδα2021 #GreekIndependence #Hellenic #IndependenceDay #Greece200 @MIT @Harvard #BU #Tufts #NEU

Excited and grateful to be inaugural recipients of a @BiswasFamilyFdn Transformative Computational Biology Grant w/ @MarinkaZitnik & Brad @PenteluteLab at @MIT & @HarvardMed. Our goal: #AI for #GenomicMedicine: #DiseaseCircuitry, #DrugDevelopment, #Personalization. Including: (1) #SingleCell #MultiOmics for target selection; (2) #GeometricDeepLearning for therapeutic design; and (3) #HighThroughputChemistry for drug optimization. $15 million awarded w/ @anshulkundaje, @marinkazitnik, @pranavrajpurkar, #KatiePollard Info: biswasfamilyfoundation.org/f… A wonderful day for #SciencePhilanthropy #Thanks!!

Congratulations to Aviv Regev for her induction in the National Academy of Sciences, a much deserved honor! @theNASciences @BroadInstitute @MIT @ScienceMIT @MITBiology

Excited to share our #SingleCell dissection of #Huntingtons Disease, showing distinct #striatum direct-vs-indirect-pathway projection neuron vulnerability in human and mouse #iSPNs #dSPNs #Neurodegeneration @MIT #Heiman Paper: nature.com/articles/s41467-0… News: news.mit.edu/2023/huntington…

Congrats to #AvivRegev who will lead @Genentech Research & Early Development. Great collaborator & friend, she helped shape the current @BroadInstitute. Her loss will be greatly felt in our community but her impact will only grow in industry. Best of luck! globenewswire.com/news-relea…

Here's my #DarwinDay lecture, on the 20th anniversary of the #HumanGenome Project, linking #AncientGreece, #CharlesDarwin, #GregorMendel, #ComplexTrait Inheritance, #PolygenicDisease, #DiseaseCircuitry, #Epimap and #SingleCell #Genomics piped.video/rmg50fOwEB4 Happy #Darwin Day!

Uh-oh... 144443 citations. This is where you drive ever-so-slowly to catch 144444 on the dashboard (but invariably miss it). Okay, back to that grant report [adding our latest papers]. No distractions, already past 5am, kids waking up soon, whoosh... scholar.google.com/citations…

Our new @GenomeResearch paper reports hundreds of new protein-coding genes in human, mouse, fly, worm & mosquito, including 118 protein-coding genes/exons overlapping previously-non-coding #GWAS hits. Eg. new eye-specific TJP2 exon associated with #myopia genome.cshlp.org/content/ear…

The Greek-Turkish friendship behind the Pfizer-BioNTech vaccine that could save the world. Very inspiring story of immigrants with dreams, drive, perseverance nyti.ms/32wbPVS #COVID19 #Vaccine #Greece #Turkey #Immigrants #Pfizer #BioNTech @AlbertBourla @BioNTech_Group

HiDRA: Building on Sharpr-MPRA+STARR-Seq+ATAC-Seq to dissect millions of human regulatory regions in one experiment biorxiv.org/content/early/20…

It's amazing how cordial and kind a critic can be in a face-to-face private conversation (eg. offering feedback after a seminar when others are *not* watching), and how the language changes to almost performative insults, as soon as that same otherwise-kind person goes on twitter piling on a mob of negative comments. Psychologically, it might be similar to the nasty comments someone could make in a living room of "buddies" in front the TV showing a politician they disagree with. Insults reinforce each other, and normalize each other, to the point of unrecognizable when taken out of that context. The difference on twitter is that the targeted person (yes, an actual person, like @NiklasGrimm824 points out) can read your insults. In the case of students, trainees, and of course professors (who are human too, lest we forget), this can be really hurtful and demoralizing. I know students (amazing students!) who have simply left science because of some very specific characters (you know them!) and their vitriol on twitter, and it's shameful and devastating to our field. It takes great effort to respond with kindness and lend a listening ear to such insults, instead of the more visceral reactions of fight (insult back, dig down, pass the nasty tone forward) or flight (leave twitter, leave science, block). But when I do respond, including in this case, I find with delight that the original poster is sometimes able to go back to more kindness and conversation, and sometimes better explain the original source of their concerns, leading to better understanding of what the actual issue was, and corrective steps to explain it, fix it, or improve upon it, instead of just dismissing or digging down. When the critic packages their critique in an insult, it's easier for the critiqued to dig down, because agreeing with the critique would imply agreeing with the insult. Then an impasse is created, making it hard to actually improve the work (or the field), give credit to the original critic (for their otherwise valuable comment), and leave corrected and enriched on both sides. If the critic instead packages their comment in kindness, first praises the good parts** (thus establishing that they're not here just to score points, see next tweet), points out a specific mistake/shortcoming that can be fixed/improved, and then suggests specific improvements, it's easier to have a conversation, by isolating the specific criticism from the overall self-worth of the original authors, and improve on the specific point, because it's not tied to any ad-hominem attacked, and thus can be let go of. Aesop's Fable of the North Wind and the Sun comes to mind, in getting a traveler to change their mind with kindness, not force en.wikipedia.org/wiki/The_No…

New podcast conversation on the #FutureOfAI, from ChatGPT to #AGI, how #AI is transforming #business, #medicine, #DataScience, and #collaboration: piped.video/watch?v=vm7KXWEp… We dive deep into the evolution of AI and representation learning, visual data landscapes, human-AI collaboration, multimodal foundation models for biology and medicine, visual AI, human-centric design, not leaving serendipity to chance, and a lot more. For the @MIT @MIT_CSAIL @CSAIL_Alliances podcast with the awesome @KaraEMiller. Eager to hear your thoughts! #MIT #CSAIL #Podcast #AGI @MIT_CSAIL @MIT @MIT_SCC @MITEECS @BroadInstitute @MIT_Picower

Excited to share our #MetabolicResilience & #GenomePlasticity preprint biorxiv.org/content/10.1101/… by @LeandroAgudeloZ @RTuyeras #TeresaFemenia #Obesity #Adaptation #Condensates #HumanAccelR #ChromatinArchitecture #Metabolism #Fasting #PGC1A #PhaseTransition #Environment #Metabolism

Truly grateful for my extraordinary research team of students, postdocs, and trainees at @MIT @BroadInstitute @MIT_Picower @MITEECS @MITCSBPhD @MIT_SCC. I keep pinching myself in disbelief, working with such amazing, driven, intelligent, creative, and diverse scientists ❤️🥰🍀🎉

Some Coronavirus Advice for my friends facebook.com/manolik/posts/1… Don't panic, but don't underestimate this either. Act rationally, minimize the spread to protect others, enjoy time with your loved ones, and act as if it's a pandemic, so it doesn't become one

It was truly a pleasure to speak on #AI for #Innovation, #Genomics, and #Medicine at our @MIT #IAP class with @RickardGabriels on #FoundationModels and #GenerativeAI. So many extraordinary advances to cover, each more exciting than the other. Video here: piped.video/watch?v=pHzdw6YW… Topics touched upon: - #CNNs for #RegulatoryGenomics and #MutationEffect prediction - #GNNs for #DrugDevelopment - #Transformers for #ProteinFolding - #VAEs for #SingleCell expression - #CLIP for #MedicalImaging-#Legends - #MultiModal function-sequence-structure for #TherapeuticDesign - #CognitiveSpace navigation for #patients #EHR, #ProteinFunction, #CellState, #DrugEffects, #ScientificPapers, #Grants, #Patents, #Education, #Investment, #Discovery, #Management, #Productivity, and #Innovation. Some slides attached below, lots more coming! :-)

Such a relief to see that #ScienceIsBack on the table at the @WhiteHouse, with @JoeBiden and @KamalaHarris nominating a top-notch Science Team, with @Eric_Lander, @Maria_Zuber, @NIHDirector, @Alondra. Let the US Beacon shine again buildbackbetter.gov/press-re… buildbackbetter.gov/wp-conte…

Truly honored that @BillGates, a true giant of computing, philanthropy and human health, choose to highlight our #SingleCell work on #Alzheimers disease with @DrLiHueiTsai out in @Nature this week

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/… Photos from previous years: Easter 2023: photos.app.goo.gl/J8KhZ7T83w… Easter 2022: photos.app.goo.gl/zAake6jQwV… Easter 2019: photos.app.goo.gl/FvPP1fYsxH… Easter 2017: goo.gl/photos/CnCnmRzVnHdtao… Weather seems *perfect*, and the lambs should be ready by 12:45am, so come on time and enjoy!!

As #COVID19 cases skyrocket throughout the world, a recent #VitaminD randomized clinical trial in hospitalized patients offers hope, with #25fold reduction in ICU admissions. Our mathematical analysis indicates its results are real medrxiv.org/content/10.1101/… #Calcifediol #Córdoba

Excited to be part of the #AIrevolution episode of @PBS @NovaPBS premiering at 9pm tonight. Already here: pbs.org/wgbh/nova/video/ai-r… With @MilesOBrien, @MustafaSuleyman (@InflectionAI, @GoogleDeepMind), #YoshuaBengio (@Mila_Quebec, #TuringAward), @ManolisKellis (@MIT), @BarzilayRegina (@AIHealthMIT), #DanielaRus (@MIT_CSAIL), @LeciaSequist (@MGHCancerCenter), @XanAmini (@Themis_AI, @liquidai), and so many more! Early reviews: @WSJ wsj.com/arts-culture/televis… @MediaPlayNews mediaplaynews.com/documentar… @Journaltimes journaltimes.com/life-entert… #AI for #Healthcare #Medicine #DrugDevelopment #ClimateChange #Prosthetics #MaterialScience #Language #Games #Strategy #DeepFakes #AutonomousDriving

Traveled 5000 miles to Greece for my second #GenomeReconnects entry #BoG22 #WHBA #MostMilesTraveledCategory @CSHLPress @cshlmeetings #GenomeResearch #FavoriteShirt 👕🎽 🐶 🛶🐬🥽

For those interested in #SingleCell analyses, #ACTIONet is our main workhorse for #Alzheimers #Schizophrenia #ALS #HD and more: a multi-scale network-based archetype approach for learning cell types and cellular states in health and disease nature.com/articles/s41467-0… Out today!

Honored and grateful to be among @NIHDirector #TransformativeAward awardees w/ @Donnelly_Lab #VeroniqueBelzil & #MyriamHeiman on #SingleCell CNS dissection of #ALS #FTLD #MotorNeuronDisease #TDP43 neuropathology/neurotoxicity #genetics #epigenomics #transcriptomics #modifiers

So excited to speak at the #AthensScienceFestival 2021 next Monday on "Breaking the Code of #HumanDisease" #ASF2021 @AthensSciFest #Genomics #ComputationalBiology #AI #ML #CS #DeepLearning #Alzheimers #Schizophrenia #Obesity #HeartDisease Register here: athens-science-festival.gr/e…

Interested in #ConvolutionalNeuralNetworks #DeepLearning #MachineVision and how machines/humans can see/understand the world around us? Watch my @MIT 6.874 lecture today piped.video/watch?v=PrLwIay2… #CNNs #Brain @BroadInstitute @MIT_CSAIL @MITEECS @MIT_Picower @DavidKGifford @MITOCW

Our new @GenomeResearch paper reports the most accurate yet update of human protein-coding genes, using #PhyloCSF of 58 mammals and 100 vertebrates, MassSpec, RNA transcription, CAGE, PolyA-seq, and @GencodeGenes curators sifting through 4000+ candidates 1/6

Excited to share our Inclusive Polygenic Score (iPGS) work and iPGS+refit, out at #AJHG today by @yk_tani. We improve #polygenic prediction of #DiseaseRisk and other traits across individuals from #diverse populations/ancestries, that have been traditionally excluded from #genetic studies, using individual-level data for individuals across the #continuum of genetic ancestry. Improvements of 60% on average for African-ancestry and 18% for admixed-background individuals, and discovery of population-specific genetic effects. Paper: cell.com/ajhg/fulltext/S0002… MIT news: news.mit.edu/2023/making-gen… Tweetorial: nitter.app/yk_tani/status/1… AJHG tweet: nitter.app/AJHGNews/status/… CSAIL tweet: nitter.app/MIT_CSAIL/status… Browser: ipgs.mit.edu/

Don't miss #CarlesBoixAdsera's Poster on #EpiMap: 833 epigenomes, enhancer modules, motifs, and #GWAS dissection of 30,247 variants across 534 traits Poster #3334 at 3pm today #ASHG19 compbio.mit.edu/epimap eventpilotadmin.com/web/page…

Excited to share our #GenoBoost paper out in @NatureComms today, a flexible #PolygenicScore #PGS modelling framework for additive and #NonAdditive dominance effects, incorporating non-zero dominance effects in 40%-67% of variants across multiple traits, including #psoriasis, #RheumatoidArthritis, #gout, #IBD, #Alzheimers and more, with @YK_Tani #YosukeTanigawa at @MIT_CSAIL, and #RikifumiOhta and #ShinichiMorishita at @utokyo_gsfs_en. Paper: nature.com/articles/s41467-0… News: csail.mit.edu/news/unlocking…

Don't miss @ZunpengLiu 's #ASHG talk on #SingleCell #MultiRegion #Epigenomic dissection of #Alzheimers next in Room 207A/Level 2 (11:30am) #ASHG23 Integrate: 576 samples, 2.3M cells (1.5M #scRNA x 900k #scATAC), 6 brain regions, 30 cell types and subtypes Results: 419k regulatory elements, active/repressed compartments, Epigenome Erosion, Transposon Reactivation, Entorhinal Cortex & Hippocampus selective epigenomic vulnerability, Team: @ZunpengLiu, @__Ben_James__, @Xushen18, @Carles_Boix, #KikiGalani, #LiLunHo in @DrLiHueiTsai and @ManolisKellis labs. Very proud of the whole team at @MIT, @BroadInstitute, @MIT_CSAIL, @MIT_Picower, @MITEECS, @MIT_SCC More info: ativsoftware.com/appinfo.php… Big thanks to: @NIH, @NIHAging, @CureAlzheimers

Next #ASHG23 #ASHG talk after the break: @NaSun818 on #SingleCell #eQTLs #genetic regulation of #Alzheimers in BallroomC/Level3 (10:30am) Integrate: 427 individuals, 2.3M cells, 23 cell types and subtypes, genotypes Results: 457k sc-eQTLs, 8.8k sc-eGenes, cell-type- / conditon- specificity, interpret AD GWAS, interpret AD DEGs Team: @NaSun818, @ypp_lab, @Carles_Boix, @HouGroup_sysGxG, @yk_tani, #KikiGalani, #LiLunHo, with @DrLiHueiTsai and @ManolisKellis labs. Very proud of the whole team at @MIT, @BroadInstitute, @MIT_CSAIL, @MIT_Picower, @MITEECS, @MIT_SCC More info: ativsoftware.com/appinfo.php… Big thanks to: @NIH, @NIHAging, @CureAlzheimers

CRISPR @NobelPrize in Chemistry to @jadoudna and @e__charpentier. This is a big deal in genomics, medicine, and the world nyti.ms/3loECTo

Very excited for Carles Boix #ThesisDefense at 10am today on #SingleCell #Mosaicism #Brain #Alzheimers #Epigenomics Join us! With @MITCSBPhD @MIT_CSAIL @BroadInstitute @MIT @MIT_Picower @MITEECS @DrLiHueiTsai @Peter_J_Park @YoungRickA #PReddien #ChrisBurge Then off to @CSH #BoG22

Thrilled to speak at @NatureGenet and @NatureRevGenet webcast on #GWAS mechanism dissection on Thu@11amET with @AnnaGloyn. I'll cover #Epigenomics #Alzheimers #Obesity #Schizophrenia #SingleCell #SpatialTranscriptomics #TFs #CRISPR #HiDRA #EpiMap Join us! go.nature.com/3lVSRj3

No, SARS-CoV-2 does not integrate into your genome. No, vaccines will not change your DNA. Please help get everyone vaccinated and help put this pandemic behind us

Please join us for a public lecture and fireside chat with @ManolisKellis and @LeoAlexopoulos on #AI and the Future of #Medicine and #Innovation this coming Tue Oct 31 at 5:30pm at @NTUA (Metsovio Polytechnio) RSVP: forms.gle/LNGmY5ZDUYNQbCbr7 (for this and future such gatherings) Join remotely (zoom): tinyurl.com/AImedicineNTUA (Note: 11:30am ET, 8:30am PT, 5:30pm Greek Time) In person: NTUA Campus maps.app.goo.gl/rytrt3x2iSfT… I hope you can join us! PS: I'm in Greece for 2 days, Tue-Thu, and the other reason is still a surprise that I'm very excited to share on Wed evening #GenomicMedicine #Therapeutics #FutureOfWork #Alzheimers #Obesity #Schizophrenia #Aging #Cardiovascular #Exercise #GenerativeAI #LLMs #GNNs #PLMs

What's the #MeaningOfLife: Think, Love, Humanity, Life, Time, Family, Layers, Planet, Legacy, Diversity, Ideas, Space, Mind, Facts, Music, Laughter, Giving, Sharing, Feeling, Connected, and 42, at least according to our #Podcast #WordCloud with @LexFridman piped.video/watch?v=bgNzUxyS…

Article: nature.com/articles/s41586-0… Perspective: nature.com/articles/d41586-0… News & Views: nature.com/articles/d41586-0… Big congrats to an amazing team led by @DrLiHueiTsai @JoelWBlanchard1 @Leyla_Aakay @_JoseDavila @DjunaVM. Truly grateful to be part of this extraordinary collaboration

Meaning of Life Symposium @MIT. Scientists, Humanists, and Luminaries reflect on the Meaning of Life, from the human scale to the cosmic scale. Blending neuroscience, philosophy, evolution, astrophysics, spirituality meaning42.com Wed 3/13/2019, 4pm-8pm 34-101. Join us!

Congrats #KellisLab, with 4 platform presentations, 1 Epstein award winner, and 5 posters, all by #trainees at #ASHG22 Each talk/poster in the thread below 🧵 Congrats to @__ben_james__ @Xushen18 @yk_tani @boix_carles #ChristianHwa & the whole team! Proud & grateful 🧑‍🎓👩‍🔬💻🧪🧬

For those wondering if #COVID19 shutdowns were needed. New study estimates they prevented 530M infections, 62M cases (i.e. 5M deaths, with CFRs lower than Italy's overrun hospitals). This is not over. Stay home, stay safe, avoid gatherings, wear your masks nature.com/articles/s41586-0…

Excited to speak at the #FestivalOfGenomics #FOGBoston at 2:20pm-2:50pm today [Secret Stage] on #SingleCell dissection of #DiseaseCircuitry. Info: connect.frontlinegenomics.co… Speakers: festivalofgenomics.com/bosto… Program: festivalofgenomics.com/bosto… Eager to re-connect with many friends old and new in this exceptional gathering... Do message me and come say hi. Also, let me know if you're interested in joining a few of us for dinner/socializing tonight.

Excited to share our research on #SingleCell dissection and manipulation of #Disease circuitry for #Schizophrenia #Alzheimers #Obesity #Exercise #Cancer #Epigenomics #SpatialTranscriptomics #eQTLs #ALS #Microglia #GWAS #EHR #Aging #EpiMap Watch here: piped.video/watch?v=tOVLwLTc…

This is embarrassing science denialism. Yes, we would certainly prefer that mental illness is not genetic, but it is. How does one respond to such pieces? madinamerica.com/2022/12/sch…

Looking for gifted programmers of all ages (including high-school!) to join our #AI team building a full-featured human-driven AI-powered data-science cognitive cartography workbench. Also seeking cartographers, navigators, and partners across diverse fields of data science. If you know (or are) a talented programmer who wants to change the world of data science with AI, please reach out! (Please send CV, GitHub, Portfolio, Slides, Goals, Interests to kellis-admin@mit.edu thanks!)

Outstanding news article by the always-insightful @AlzForum on our #SingleCell #MultiRegion study of #Alzheimers Disease. Thanks for the wonderful coverage of our work! alzforum.org/news/research-n…

Don't miss our four #ASHG20 talks today/tomorrow on #SingleCell dissection of #Alzheimers #Obesity #Exercise #Schizophrenia using #scRNA #scATAC #GWAS #eQTLs #Mosaicism Big congrats to #MariaKousi #AustinWang #XushenXiong #JackieYang and our collaborators!

Just made a donation to IITMAANA to support India Covid-19 Relief. This is a trusted effort that I have received personal vouching for by Hari Balakrishnan at MIT, run by his personal connection Mohammed Siddique, head of Chennai COVID management efforts iitmaana.nationbuilder.com/d…

Couldn't be happier for #science and its return to the US presidency agenda. @Eric_Lander is perfect for the role, and being part of the @JoeBiden Cabinet is a big deal. Our country needs this badly. Congratulations!! #ScienceIsBack

My #CompBio class is starting again @MIT next week. #MachineLearning for #Genomics: Dissecting Disease Circuitry. Overwhelmed by the #OnlineLectures support last year. I hope your students can join in person this year! nitter.app/manoliskellis/status/1… More info: compbio.mit.edu/6.047

Do you know/have/are high-school students interested in #AI for #DataScience? We've developed a 5-session course with @therobohub for 5 Saturdays from Oct 19-Nov 16, covering (1) data science, (2) predictive modeling, (3) AI agents, (4) data scraping, and (5) the integration of AI in real-world business models. Spread the word! hisawyer.com/the-robo-hub/sc…

Excited to present our #SingleCell dissection of #Alzheimers #Schizophrenia #Bipolar #Huntingtons at #ASHG19 800 Brains, 5.5M cells #scRNA #scATAC #scQTLs 4:15pm today Level3/BallroomB Session029 Talk52 ativsoftware.com/appinfo.php… with @DrLiHueiTsai #MyriamHeiman #BradRuzicka #ROSMAP

Tomorrow is not about politics, it's between lies and false promises vs. truth and action. Let's #vote populism out and bring the US back to reality. Let's invest in science, research, infrastructure, progress, and let the Beacon of the World shine again facebook.com/manolik/posts/1…

Today I responded to the #TakeYourShots challenge. Spread the word about #VaccinesSaveLives, and drink a shot of 1 lemon. Nominate at least 5 others. I nominate @Eric_Lander @GeoChurch @AndrewWLo @DrLiHueiTsai @SafiBahcall @natalya926 @quantum_spiros @LRafaelReif @NIHDirector

From Genomics to Therapeutics: Single-Cell Dissection and Manipulation of Human Disease Circuitry vimeo.com/775875318/723f5f61… My talk at @GenomicsEngland #DiscoveryForum Slides here (w/QR codes): dropbox.com/s/tpn0o94ysqmr4f… #Alzheimers #Obesity #Disease #TeamWork

My views on the #MeaningOfLife, horizontal and vertical evolution, the importance of diversity, the danger and fallacy of eugenics, the horizontal transfer of knowledge through humanity and fellowships, and the evolution and sharing of ideas piped.video/watch?v=XofjTAyG… March 13, 2019

Really looking forward to #RECOMB2024 this week, and reconnecting with the #ComputationalBiology community joining us at @MIT @Harvard @HarvardMed @Tufts @BroadInstitute #BU #NE and more. This is one of the most successful RECOMB meetings to date, with near-record registrations. Don't miss it. You can still register here: recomb.org/recomb2024/regist… Outstanding line-up of invited and contributed talks from leaders of the field and trainees alike, and most importantly, and amazing opportunity to network across #academia, #industry, #pharma, #hospitals, #healthcare, #AI, #CS, #Algorithms, and #MachineLearning, in arguably the most vibrant #CompBio community in the world. And don't miss the RECOMB satellite meetings #Cancer, #SequenceAnalysis, #Genetics, #Bioninformatics #Education, and #ComparativeGenomics. Spread the word, register now, and see you there!! recomb.org/recomb2024/regist… PS: Oh, and did I mention the #Gala at the @MuseumOfScience on Tuesday?

Really honored and proud to speak at the @HarvardMed #PostdoctoralFellows program, with the #HMS Biomedical Sciences Program #BSCP, the Diversity Inclusion and Community Partnership #DICP, and the HMS Black Postdoc Association #HBPA. #Diversity is the bedrock of our community, and I'm a proud #immigrant working with many #FirstGeneration students from multiple #ethnic and #cultural backgrounds including Hispanic/LatinX, African American, Asian, European, and more. We discussed #AI for #BiomedicalResearch, and how this extraordinary convergence of technologies and people is changing the world for the better bscp.org/ hbpa.hms.harvard.edu/ dicp.hms.harvard.edu/

How badly are we underestimating #coronavirus cases in the US? Probably 150-fold (5000 diagnosed, 750,000 actual). Quick analysis on 3/19-3/20 numbers, doubling rate (3 days), incubation (20 days), death rate (1%): facebook.com/manolik/posts/1… So stay home, the only param you control!

So honored to be back in Athens, speaking at EmTech Europe (Emerging Technologies) on "The AI Frontier: Transforming Health, Knowledge, and Human Achievement" on Thursday morning at 9:45am Greek Time. The talks will be live in person at the stunning Megaron Athinon Concert Hall, and will also be video broadcast for online registrations. Excited to join fellow MIT alumni on Wednesday evening, and to be staying at the footsteps of the Acropolis in the Herodion hotel (the photo is from my room!). Stunning line-up of visionary speakers, including multiple colleagues and friends. Please let me know if you're in town in Athens, and let's meet up for dinner or a tour of the Acropolis, Plaka, Monastiraki, my beloved hometown, and its stunning history spanning thousands of years. Register here: emtecheurope.com/ and do message me to catch up!

Excited to speak at #CMU #CS #CompBio at 1pm today (in person and on #zoom). #AI for #GenomicMedicine: #SingleCell Dissection and Manipulation of #DiseaseCircuitry 1pm at GatesHillman GHC 6115 Zoom link: cmu.zoom.us/j/98431590345?pw… Info: cs.cmu.edu/calendar/17029989… Hosts: @jmuiuc and #RussellSchwartz Stop by to say hi!

So excited to speak next at the European #Atherosclerosis Society Congress in the closing plenary session. So many parallels across #cardiac, #obesity, and #Alzheimers with #lipids, #cholesterol, #vasculature, #immune/#monocyte/#macrophage/#microglia dysregulation, #metabolism, #endothelial, oxphos, #inflammation, highlighted across #genetics, #genomics, #SingleCell, #SpatialTranscriptomics, and #EHR phenotypes integration. #EAScongress2023 @EASCongress #MyEAS23

Thanks for the kind words Rik. It's hard to please everyone. If a paper has too little data, someone will criticize the lack of transparency. If it has too much, someone else will comment that it's overwhelming. [Sometimes it's the same person too]. Best way to avoid their criticism: do nothing. Anyways, I'm very proud of my students' wonderful contributions to science, and I hope this negativity on twitter/X by some recurrent characters doesn't get under their skin. I wish it didn't get under mine. Love to all! <3

My #TEDx talk at @TEDxCambridge on "Decoding a Genomics Revolution" was a 10-min crash course on #genomics piped.video/zlVZ0ORtpPM Super excited to speak again at #TEDxMIT on Dec 4th. What should I talk about? :-) Requests welcome!