Vince Buffalo @vsbuffalo
Evolutionary genetics postdoc @UCBerkeley ♥s biology, running, probability+statistics, 🦀, fly fishing, backpacking. Author of book Bioinformatics Data Skills vincebuffalo.com Berkeley, CA Joined August 2009-
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I really enjoyed this paper by Wakeley et al. (2023), working out the sampling theory for latent mutations (recurrent recent mutations indistinguishable from other copies) in the ancestry of a rare variant. academic.oup.com/genetics/artic…
I think there is a huge benefit to standardizing a chunked on-disk binary typed arrays (e.g. Zarr) to store VCF data. Then, build bioinformatics and population genomics software on top of this format. bio2zarr is alpha but I'm very excited: github.com/sgkit-dev/bio2…
I wonder how many bugs are introduced into science annually just because the default software installs on clusters are often quite outdated. I'm lobbying our IT to update bcftools from 1.6 to 1.20 — 1.6 is from 2017!
No SMBE talk 😢. 3/3 abstracts I’ve submitted for talks have gone to posters. Quite dispiriting as a postdoc.
An original manuscript page by Richard Feynman in which he mentions the first-order Runge-Kutta method for approximating the solution to a differential equation. He includes a sequence of computer commands and a flow diagram for a computer to perform acceleration calculations:
An original manuscript page by Richard Feynman in which he mentions the first-order Runge-Kutta method for approximating the solution to a differential equation. He includes a sequence of computer commands and a flow diagram for a computer to perform acceleration calculations: https://t.co/uIuysFYUIY
Wow, Snakemake 8 really fudged up Slurm support. Good grief.
Congratulations Alison Etheridge of @UniofOxford, newly inducted NAS international member! #NAS161 #NASmember #mathematics
FIRE is deeply concerned by law enforcement actions to detain student protesters at Emory University, including the deployment of tear gas and tasers. While colleges may restrict conduct — such as establishing encampments — that violates reasonable, viewpoint-neutral policies,…
New paper from the lab! Epigenetic silencing of transposons is widely considered a good resolution of host-TE conflicts, but is it? Especially, we showed that this silencing could lead to harmful local enrichment of repressive marks, even in genes (Huang et al. 2022 eLife). (1/5)
New paper from the lab! Epigenetic silencing of transposons is widely considered a good resolution of host-TE conflicts, but is it? Especially, we showed that this silencing could lead to harmful local enrichment of repressive marks, even in genes (Huang et al. 2022 eLife). (1/5)
“The muscle of independent thinking and open debate, the ability to earn authority that Daniel Bell described as essential to a university’s survival, has long since atrophied.” theatlantic.com/ideas/archive/…
Cultural Revolution in China, Iranian Revolution, Hitler Youth in Germany, Khmer Rouge (which led to the Cambodian genocide) all had student support against the ruling class. University activists must actually study history at their universities, and not just engage in activism.
Cultural Revolution in China, Iranian Revolution, Hitler Youth in Germany, Khmer Rouge (which led to the Cambodian genocide) all had student support against the ruling class. University activists must actually study history at their universities, and not just engage in activism.
How do cells efficiently respond to stress? Transcriptional stress responses are well-known—and in our latest study, we discover that cells use biomolecular condensation to redirect translation from old to new mRNAs 1/n biorxiv.org/content/10.110…
The trip from SAN to SFO is probably the prettiest flight I’ve taken. The descent zigzags up the coast and peninsula of California.
A major threat to Mojave desert tortoises is the massive growth of raven populations (index from Harju et al. 2021), which take advantage of anthropogenic structures to build nests. Baby tortoises are yummy raven snacks.
A major threat to Mojave desert tortoises is the massive growth of raven populations (index from Harju et al. 2021), which take advantage of anthropogenic structures to build nests. Baby tortoises are yummy raven snacks. https://t.co/iQdAyAOlbz
Matthew Hahn @3rdreviewer
12K Followers 572 Following Population geneticist. Hobbies include: two kids.Andrew Kern @pastramimachine
15K Followers 4K Following Evolution, population genetics, machine learning. rhythm section. he/himGraham Coop @Graham_Coop
20K Followers 3K Following Popgen @UCDavis. @[email protected] . Tweets, grammar, & spelling are my views only.He/him. #OA popgen book https://t.co/R6I2dcaEGfMing "Tommy" Tang @tangming2005
30K Followers 2K Following Director of computational biology. On my way to helping 1 million people learn bioinformatics. Educator, Biotech, single cell. Also talks about leadership.Lior Pachter @lpachter
44K Followers 2K Following Bren Professor of Computational Biology @caltech. Blog at https://t.co/FFQzhEsmhi. Tweets represent my views, not my employer's. #methodsmatterJoshua G. Schraiber�.. @jgschraiber
8K Followers 8K Following Evolution, statistics, software, slacktivism. Once left a tenure track job, but trying to get one again. @docedge85 and @mwpen pay my billsDmitri Petrov 💔 @PetrovADmitri
15K Followers 4K Following Evolutionary Biologist at Stanford. Rapid Evolution, Adaptation, and Genomics. Open Science advocate.Jeffrey Ross-Ibarra @jrossibarra
12K Followers 3K Following evolutionary genomics of maize. erstwhile ethnobotanist. purveyor of bad puns. dad. not a cool cow from 1994 (he/him) @[email protected]Liam Revell @phytools_liam
9K Followers 2K Following Evolutionary biologist, R developer, & occasional heterodox. Tweets mostly about phylogenetics... but sometimes speech, the academy, politics, & COVID.Michael Love @mikelove
18K Followers 5K Following I'm not on twitter anymore, find my on Bluesky or MastodonAnshul Kundaje (anshu.. @anshulkundaje
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23K Followers 7K Following Chair, Comp Bio & Medicine Program, Princess Margaret Cancer Centre. Assoc Prof, Med Biophysics & Comp Sci, University of Toronto. COI https://t.co/CvupKNIjZrMick W@tson ↙️ @BioMickWatson
30K Followers 3K Following Bioinformatics | (meta) genomics | Data science. Some politics. Views are all my own and do not represent past, current or future employer.Heng Li @lh3lh3
10K Followers 207 Following Associate professor of biomedical informatics at @HarvardDBMI and @dfcidatascienceAlex Harkess @aeharkess
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60 Followers 151 Following PhD candidate in Biotechnology | Evolutionary ecology - Experimental evolution - Extremophiles 🌋 Fundación Ciencia y Vidamar 🇵🇸🪸🫧 @marmarinn
247 Followers 1K Following ella/she. amor, rabia y esperanza 🌱🔥 participo en @AsambleaEpop | yofkaSophie Belman @BelmanSophie
373 Followers 374 Following @SchmidtFellows | Postdoctoral scientist @BSC_CNS | disease dynamics in climate context | https://t.co/8VFOidn9BL | Previously @sangerinstituteGrog Goose @groggoose
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201 Followers 310 Following Cancer Evo & #rstats Enthusiast @ASU • Grad Research Assistant @ACE_Arizona @MaleyLabAlex Lee @lee___alex
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63 Followers 275 Following RA in Synthetic Data Generation @turinginst | ex-UCL RoboticsHaowen He @HaowenHeCompbio
1 Followers 85 Following PhD student @GeorgiaTech | computational biology & single cell genomics 🧬 💻🧮David McCarthy @DAVIDMAPENZAUS1
1K Followers 5K Following Mr Nice Guy|| Retweets are not an endorsement.Lucas Waldburger @LucasWaldburger
248 Followers 956 Following PhD student at UC Berkeley, NSF research fellowTessa Ferrari @TessaFerrari
12 Followers 81 Following Lab tech studying population genetics at the USC Mooney lab @Jazlyn_Mooney @qcb_usc 🧬👩🏻💻📊📚 ✌️🎓 B.S. in Quantitative Biology @USC 2023The Romanian Reaver @RumanianReaver
4 Followers 425 FollowingSmart Cherrys Tech @smartcherrystc
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889 Followers 1K Following Postdoc in the @WagnerEvolution lab interested in enhancers, promoters, developmental biases, and de-novo emergence. Opinions are my own. He/him. 🏳🌈Salem Belkessa @belkessa_salem
461 Followers 3K Following Ph.D. Mouloud Mammeri University of Tizi Ouzou, Algeria 🇩🇿. Interested in Host-pathogen interactions, Gut microbiome, Parasitic diseases.Sanja Savel @sanja_savel
0 Followers 123 FollowingSunishka Thakur @sunishka_
123 Followers 129 Following PhD student in the Cummings lab at UT Austin. she/her 🇮🇳MaggieBart @smcMlc5t7U8J3
3 Followers 112 Followingsanjana curtis! 🦦 @sanjanacurtis
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555 Followers 3K Following Dad | Lifelong Student | Water Tech | Sustainability | Circularity | Net-Zero | Automation & AI | @ArcadisGlobal Views=MineAngie @Angie8665345919
5 Followers 245 FollowingBetsy Gibson @BetsyGibso1
10 Followers 230 Following When we forgive we heal, when we let go we grow, your life is just result of little choices you make.Saxon E. Musk @saxon__musk
133 Followers 742 Following Am Saxon musk The son of Elon Musk CEO of twitter (X) and Tesla 🚀🚀🚀🇺🇸Kimberly Moser @chittlin
33 Followers 101 Following I’m an old, weird scientist. Currently studying evolutionary development in C. inopinata and it’s relation to C. elegans - starting with body size.jeff konen @konen_jeff
7 Followers 743 Following "Learning is the only thing the mind never exhausts, never fears, and never regrets." — Leonardo Da VinciGlycodepot @glycodepot1401
2 Followers 463 FollowingGayathri Iyer @Gayaisbrown
86 Followers 3K Followingsselection42 @sselection42
384 Followers 2K FollowingReasonable Doubt @Redoubters
20 Followers 223 Following Mistakes were made. Fantasy and politics, not necessarily in that order. Chronicle of Astreia novels coming... sometime. Really hate Nazis.Sachin @Smrathod_23
2 Followers 86 FollowingSarthak Chauhan @SarthakCha72294
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2K Followers 820 Following comp bio, human genetics, long reads — hiking, skiing, climbing. Senior CompBio manager at @pacbio; views are my own.Z @Znemisis__
23 Followers 190 FollowingCahterina Rivas @Cahterina51
177 Followers 2K Following 📍Rome, Italy 🇮🇹 Surgeon Doctor 👩⚕️ Working With @who I Love Flowers 💐 My Moto Is To Provide A Healthy Life For YouPensé FFun @inftyCategory
100 Followers 6K FollowingMatthew Hahn @3rdreviewer
12K Followers 572 Following Population geneticist. Hobbies include: two kids.Andrew Kern @pastramimachine
15K Followers 4K Following Evolution, population genetics, machine learning. rhythm section. he/himGraham Coop @Graham_Coop
20K Followers 3K Following Popgen @UCDavis. @[email protected] . Tweets, grammar, & spelling are my views only.He/him. #OA popgen book https://t.co/R6I2dcaEGfMing "Tommy" Tang @tangming2005
30K Followers 2K Following Director of computational biology. On my way to helping 1 million people learn bioinformatics. Educator, Biotech, single cell. Also talks about leadership.Lior Pachter @lpachter
44K Followers 2K Following Bren Professor of Computational Biology @caltech. Blog at https://t.co/FFQzhEsmhi. Tweets represent my views, not my employer's. #methodsmatterJoshua G. Schraiber�.. @jgschraiber
8K Followers 8K Following Evolution, statistics, software, slacktivism. Once left a tenure track job, but trying to get one again. @docedge85 and @mwpen pay my billsDmitri Petrov 💔 @PetrovADmitri
15K Followers 4K Following Evolutionary Biologist at Stanford. Rapid Evolution, Adaptation, and Genomics. Open Science advocate.Jeffrey Ross-Ibarra @jrossibarra
12K Followers 3K Following evolutionary genomics of maize. erstwhile ethnobotanist. purveyor of bad puns. dad. not a cool cow from 1994 (he/him) @[email protected]Liam Revell @phytools_liam
9K Followers 2K Following Evolutionary biologist, R developer, & occasional heterodox. Tweets mostly about phylogenetics... but sometimes speech, the academy, politics, & COVID.Michael Love @mikelove
18K Followers 5K Following I'm not on twitter anymore, find my on Bluesky or MastodonAnshul Kundaje (anshu.. @anshulkundaje
22K Followers 2K Following Genomics, Machine Learning, Statistics, Big Data and Football (Soccer, GGMU). Post: @anshulkundaje, Threads: anshulkundajeMichael Hoffman @mich.. @michaelhoffman
23K Followers 7K Following Chair, Comp Bio & Medicine Program, Princess Margaret Cancer Centre. Assoc Prof, Med Biophysics & Comp Sci, University of Toronto. COI https://t.co/CvupKNIjZrMick W@tson ↙️ @BioMickWatson
30K Followers 3K Following Bioinformatics | (meta) genomics | Data science. Some politics. Views are all my own and do not represent past, current or future employer.Heng Li @lh3lh3
10K Followers 207 Following Associate professor of biomedical informatics at @HarvardDBMI and @dfcidatascienceAlex Harkess @aeharkess
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17K Followers 1K Following Genome mutation, software for genomic discovery. https://t.co/6GKjALLFfk Co-director, DELPHI Data Science Init.: https://t.co/8uWRcIzWRrJoel McGlothlin @joelmcglothlin
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9K Followers 538 Following Antonin Scalia Professor of Law, Harvard Law SchoolJoel Grus 🤠 @joelgrus
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883 Followers 2K Following Ass. Prof. of Comp Sci at Binghamton U. Parallel computing, applied ML, science groupie. I reply/tweet haphazardly and eclectically. @kjw-chiu.bsky.socialAllen Downey @AllenDowney
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761 Followers 941 Following I work on genomics, but love all of biology and any means to investigate it with math, probability, and computation. He/him/his/they/their.Ann Gregory, PhD @gregory_annc
2K Followers 2K Following Assistant Professor at @UCalgary in the Dept. of Biological Sciences | Viromics & Viral Ecology | Views are my ownScience Wise Podcast @ScienceWisePod
124 Followers 388 Following Listening will feel like confiding in your wisest auntie, who just happens to be a badass scientist! . Hosted by Dr. Emilia Huerta-Sanchez and Dr. Rori RohlfsDarren Dahly - on Blu.. @statsepi
28K Followers 5K Following Epidemiologist + Statistician | @HRBIreland @CRF_Cork @UCCPublicHealth @UCC | #ClinicalTrials #EpiTwitter #StatsTwitter Views mineMike Famulare @famulare_mike
4K Followers 1K Following Like polio, Twitter lingers on. Learning to be a father, husband, and person. Transmission epidemiologist, see Google Scholar. All tweets mine alone.Sam Power @sp_monte_carlo
17K Followers 7K Following Lecturer in Maths & Stats at Bristol. Interested in probabilistic + numerical computation, statistical modelling + inference. (he / him)Keith Adams @KeithLAdams
866 Followers 632 Following Professor, U of BC. Genome evolution, polyploidy, duplicate gene evolution, gene regulation, alternative splicing, non-coding RNAs, Brassica, duckweedCulture Critic @Culture_Crit
1.3M Followers 998 Following Tradition is not the worship of ashes, but the preservation of fire.Raymond Hames (@rayha.. @HamesRaymond
618 Followers 373 Following Professor of Anthropology, University of Nebraska - Lincoln; behavioral ecology; evolutionary anthropology; cooperation; warfare; marriageChris Oakley @quercus62
1K Followers 1K Following Interested in adaptive plastic responses to seasonality, fitness trade-offs, climate change, maladaptation, and heterosis. Plant lover. Purdue University.Edward Tufte @EdwardTufte
110K Followers 4K Following Statistician,visualizer,artist, professor. Founded Graphics Press, Hogpen Hill Farms, ET Modern GalleryTimothy Bates @timothycbates
5K Followers 1K Following Researching IQ, conscientiousness, interests, moral foundations & human attainment. Lots of individual differences & geneticsAlexis Breen @alexisjbreen
772 Followers 760 Following Senior postdoc @MPI_EVA_Leipzig #CrowCoG co-leader #Birds #Behaviour #BayesConor Browne @brownecfm
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129K Followers 423 Following Hacker :: https://t.co/km8BR8E1Ga :: [email protected] :: PGP https://t.co/dYipV8y3bo :: @warstudies :: https://t.co/H3dWknFCfk :: https://t.co/Z2lWqEVVuaNicolas Lou @NicolasLou10
284 Followers 501 Following Postdoc with @psudmant. Former PhD student with @ntherk. Broadly interested in population and conservation genetics.Cade Gordon @CadeGordonML
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40 Followers 70 Following PhD Student with @benjaminhgood -- evolution, pop gen theory, microbesAdmiral Cloudberg @KyraCloudy
2K Followers 13 Following Kyra Dempsey | Aviation writer known as Admiral Cloudberg. I explain air accidents in detail. | Follow me on Reddit: https://t.co/3YB5TGEFo8Andrew Conway @AndrewRAConway
4K Followers 1K Following Professor and Department Head, Department of Psychology, New Mexico State University ||| Editor, Journal of Intelligence ||| 🇺🇸🏳️🌈Kevin McGrew (aka Kdi.. @iqmobile
2K Followers 2K Following #Intelligence #IQ #Psychology #IQsCorner #cognitive #psychometrics #measurement #coffeesnob #Vikings.COI-royalty interest in WJ IV battery.Jarno N. Alanko @jnal.. @jnalanko
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5K Followers 1K Following Open Access Advocate - Program Officer of Knowledge & Research Services @gatesfoundation - Opinions & endorsements are my ownTrevor Cousins @trevorcousins_
572 Followers 500 Following PhD student in the Durbin group; Uni of Cambridge. Previously (2022-2023), visiting researcher in the Reich Lab, Harvard University.Aizenman Lab @AizenmanLab
3K Followers 803 Following Neuroscience lab at Brown working on the development of synapses, neural circuits and behavior. Not official university account. Tweets by Carlos. 🇲🇽Andrew Côté @Andercot
64K Followers 1K Following engineering physicist, founder Hyperstition Inc, scout @a16z, runs @TheAISalonSF, deep-tech, physics, energy and sci-fi 🇨🇦Matt Dursh @MattDursh
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237 Followers 482 Following PhD Candidate @PrecisionMedPhD @EdinburghUni | statistical genetics | dermatogenetics | https://t.co/cs4Bm7SmCcJames Shepard @jumpjim
19K Followers 1K Following B787 Training Captain. Aviator, Tech Geek. Fascinated by Space 🚀, and Otters 🦦 . Ambassador for @Bear_Force01. Views presented are personal.Blake Scholl 🛫 @bscholl
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918 Followers 1K Following Human disease genomics, precision medicine and machine learning. Associate Professor at @IcahnMountSinaiAI Breakfast @AiBreakfast
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89K Followers 997 FollowingEvan Irving-Pease @EvanIrvingPease
876 Followers 792 Following Assistant Professor in Population Genetics @Globe_UCPH Trustee @ISBArchaeology | Fellow @LinneanSociety Archaeology | Bioinformatics | Genetics 🇦🇺🇬🇧💀🧬Colossal Biosciences�.. @itiscolossal
13K Followers 666 Following The de-extinction company. #itiscolossalBen Lamm @federallamm
19K Followers 2K Following Present: @ItIsColossal Past: Founder w/ exits to @liveperson @zynga @accenture. Love startups, science, defense, space. Fellow/Board of Trustee @explorersclubcora @KylerCora
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37K Followers 871 Following Assistant professor (of mathematics) at the University of Toronto. Algebraic geometry, number theory, forever distracted and confused, etc. He/him.Early pregnancy sucks bc you’re “not supposed to tell people” when there’s also the most barfing and brain fog so people think you’re rude weird & stupid. Sorry if I canceled or looked like I hated your idea the last few months! Proud to say I’ve only vomited on myself so far🤰🏻
@vsbuffalo Personally I dislike the symposium structure of the SMBE conference - too many niche topics; I would prefer random selection of talks, may be with weighting towards ECRs
When it comes to problems with academic publishing we are in fact the baddies. So many scholars really think pre-pub peer review works as quality control & published stuff is trustworthy. There is no easy fix to the quality problem, but ending publication as target is a beginning
This post is getting a lot of attention. I usually agree with Brian, but I disagree here in a couple issues. Not accounting for (1) growth in the number of active scientists; (2) ignoring the democratization of the participation and access to science. dynamicecology.wordpress.com/2024/04/29/the…
@vsbuffalo @sexchrlab @jrossibarra That is super valid! Fwiw, I find posters are the best for helping me think about my science. But you can do that at a local symposium to balance the life/work travel.
Seen flying over the ceremony later - seems appropriate for Karim
As someone who feels that I’m something of a fiduciary for my students, a lot of these videos make me feel as though the national media and public figures are encouraging these kids to make some bad decisions that will impact them for a long time.
@rossbiology @vsbuffalo @jrossibarra (I digress) I remember watching a super famous scientist in the last half day of a session at ASHG. 7000 people registered and there were only 4 of us in the audience. 😱 But also, poster sessions can be poorly attended.
@vsbuffalo @jrossibarra That's true. I think the networking is super important and you have a chance to talk to people more at a poster than a talk, depending on the poster session/talk. Though talks are more prestigious. I feel weird about, "if I don't give a talk it isn't worth attending" mentality.
@vsbuffalo @jrossibarra Why? All the networking and learning/reading.
I’m an Arab-Muslim at Yale. Here’s why I think that calls for divestment miss the mark. 🧵
Updates! I'm still researching KAL 007 but it's taking a while. In the meantime I discovered a bizarre but fascinating little incident that should turn into a new article to release in the next couple of days...
Attending the memorial this PM
Today, April 29th is the Day of Remembrance for Karim Abou Najm, the UC Davis student who was fatally stabbed in Davis last year. He was six weeks away from graduating with a bachelor’s in computer science with honors. 🔗 Program & Register: bit.ly/3QsK1un
@vsbuffalo Come to SSE/ESEB in Montreal 🙂 I'd be excited to hear your latest!
@vsbuffalo I have four publication at MBE. One a certified highly cited paper. Still never have given a talk at SMBE. I love the society but man....
@vsbuffalo I somehow got a talk at SMBE as a first year grad student. It was in a symposium that had nothing to do with my work, predictably went bad, and then I think proceeded to go 0/8 with talks there afterwards. Still my favorite conference though!
@vsbuffalo I agree - I think the key conferences in each field have an obligation to help people during key transitions: undergrad->grad, grad->postdoc, postdoc-> faculty/industry, assistant professors -> tenure.
@vsbuffalo I've been there, when this happened I invited specific people to my poster and made some meaningful connections
@vsbuffalo That is the curse of bioinfo, unfortunately. Publish paper, forget about software. And I don't think CI/CD is a thing in the field, so many years later. Thus critical skills for soft maintenance are lacking.
@vsbuffalo Welcome to the club! I'm 4/4 on SMBE posters 😅 Thankfully I've gotten a pair of talks at other meetings, but would have loved to give one at SMBE