Matthew Stephens @mstephens999
Professor in Statistics and Human Genetics at University of Chicago stephenslab.uchicago.edu Chicago, USA Joined May 2012-
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Glad to see our paper, with @xinhe2 @mstephens999 @wescrouse Sheng and Kevin, is out today at @NatureGenet! nature.com/articles/s4158…. We developed a new statistical method, causal-TWAS or cTWAS, to reliably identify causal genes in genome-wide association studies (GWAS). 1/n
The Department of Human Genetics at University of Chicago is searching for a faculty candidate in Computational genetic and genomics. Please share this job ad with your colleagues: apply.interfolio.com/127605
My PhD work "On the Genes, Genealogies, and Geographies of Quebec" is now published in SCIENCE!!🧑🔬 🌎We explore the emergence of genetic variation in Quebec's settler population with a detailed model using a genealogy of 5M records. 🔗science.org/doi/10.1126/sc… 🧵for details : 1/7
recent work from my lab on applying and interpreting topic models for single cell data: biorxiv.org/content/10.110…
PLZ RT: I’m happy to present @nmancuso_ Lab’s new software SuShiE (Sum of Single Shared Effects) that performs variational SNP fine-mapping on multi-ancestry molecular QTL data. Stay tuned for the future manuscript! (1/8) github.com/mancusolab/sus…
I missed tweeting this when posted in Dec. Our attempt to ameliorate some problems with confounding in TWAS. Key idea is to compete (imputed) gene expression and SNPs against one another as explanations for an asssocation. biorxiv.org/content/10.110…
Pleased to share our latest preprint. We extended the SuSiE model originally developed by the @mstephens999 Lab to a cross-population fine-mapping method. Led by the talented @KaiYuan1990 with @hailianghuang @RyanLongchamps @AFPopgen + many others. medrxiv.org/content/10.110…
Glad to see this implementation out! We extended the SuSiE model to latent factors with SuSiE-PCA! Using JAX, SuSiE-PCA can run on CPU, GPU, or TPU. Preprint to come shortly, but in meantime, please try it out for your high-dim data settings and share your thoughts!
"Poisson-mash", or how to detect gene expression differences in multi-condition experiments (from the group of @mstephens999, together with Nicolas Chevrier and colleagues). arxiv.org/pdf/2210.00697…
Thanks so much @JovMaksimovic for sharing with us your love for #workflowr and huge thanks to the #workfowr developer @jdblischak for this incredible & easy to use tool that is helping the community towards better analyses & science! Find talk slides github.com/R-LadiesMelbou…
So, this came out ..
We have a new open-rank faculty search in the department of Medicine at the University of Chicago! We are looking for PhD scientists in a wide range of research areas. Please share widely. academicjobs.uchicago.edu/positions/1029…
The University of Chicago, Department of Human Genetics, is searching for a new computational faculty. apply.interfolio.com/112673 We are a small, friendly department doing top-quality science. Come join us! (Please RT)
NIH peer review system is far from perfect, but it's the best I've seen. I just "retired" from the GCAT study section after 4 years' of service, which prompted me to share a few thoughts re computational proposals. These are the points that I also remind myself. Other thoughts?🧵
Gil Mcvean on the interpretation of PCA applied to population genetics data journals.plos.org/plosgenetics/a…
@random_walker @GaryMarcus FWIW this paper wildly overstates the problem: PCA is an exploratory data analysis tool with well-known theoretical properties journals.plos.org/plosgenetics/a…
📢Big news: my lab is moving to @UChicago! I'm thrilled to join the superb genomics and microbiome research community at UChicago, and beyond excited about new research directions and collaborations! And we're recruiting at all levels! 👇 blekhmanlab.org
Ask yourself which 2-D representation better represents the structure of the hypercube. An orthogonal projection or t-SNE?
Ask yourself which 2-D representation better represents the structure of the hypercube. An orthogonal projection or t-SNE? https://t.co/GOZOdLnxku
Our bioinformatics team at Center for Research Informatics at U Chicago is ever-growing. cri.uchicago.edu/bioinformatics/ Now multiple scientist positions are available. Please check us out if you are on the job market. See below post for details.
Anshul Kundaje (anshu.. @anshulkundaje
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Veera Rajagopal @doctorveera
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Vince Buffalo @vsbuffalo
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Joshua G. Schraiber�.. @jgschraiber
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Nicholas Mancuso @nmancuso_
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Howard Duan @HowardDuan345
2 Followers 22 Following
Yin-Hong Cao @caoyinhong
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128 Followers 468 Following Studying hormone signaling in ER+ breast cancer in Brisken's lab at EPFL. Mathematician. Newsletter: https://t.co/q3u5xgysOa
Erik L Sparks 🇺�.. @ELSparks
356 Followers 3K Following SSG Orion N. Sparks WA 29 KIA 26 September 2012
HuskyLoverPt2 @HuskyLoverPart2
11 Followers 273 Following I have returned! Formerly, I posted here as @KarolynFox32493 here on X, with similar contents both original & reposted
Chandramauli Chakrabo.. @ChandramauliCh4
101 Followers 1K Following Pursuing B. Stat course from ISI, Kolkata. Interested in chess, classical music and instruments (play the Esraj) and all the random stuff.
Chloe Slaney @slaney_chloe
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Tim Lau @timlautk
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Xuebo Wang @PoffTuan
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Robert Klitgaard @RobertKlitgaard
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Javier Maravall Lópe.. @javier_maravall
9 Followers 109 Following PhD student in the Reich lab @Harvard. Interested in human population, evolutionary and statistical genetics.
Chengzhong Ye @chengzhong_ye
9 Followers 71 Following Statistics PhD student @UCBerkeley working at the intersections of statistics, machine learning and biomedicine.
Xu Huixin @WinnieHuixinXu
1 Followers 64 Following
Xiaohe (Lucy) Tian @xiaohetian89
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Jujiao Kang @Jujiao_Kang95
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Grace Miller @XBai12312767
22 Followers 653 Following life is too short so that we should use time with someone who love us from their heart it's better than using time with someone who never take care for us
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106 Followers 1K Following Likes paleontology, anthropology, and related sciences. English Lady.
British Research Pane.. @BritishPanel
254 Followers 577 Following The British Research Panel is a community of patient volunteers. We aim to promote the research and development of new medicine for a variety of illnesses.
Robert Corty @rheumrob
414 Followers 937 Following fellow in rheumatology interested in the cause(s) of auto-inflammatory diseases
Mark Caughey @MarkCaughey2
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Marathon.Beh @BehMarathon
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213 Followers 920 Following Data Analyst | Freelancer | Blogger | Shorts and Reels Video Editor | Content Creator email ✉️: [email protected]
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Y.C. Su @suyanchi
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Pavitra Muralidhar @pavitra451
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Tetsuya Yamada-Saito @TYamadatt
123 Followers 614 Following Ph.D. student @kaessmannlab @ZmbhH @UniHeidelberg
Timothy Raben @TimothyRaben
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Wentao Cai @WentaoCai148297
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Joel Slade @SladeLab
39 Followers 207 Following Bird nerd. PI of the Slade Lab (avian ecoimmunology) at Fresno State. Posts and opinions are not those of my employer.
Fangzhi Luo @abcghi123567
24 Followers 120 Following Phd in biostatistics, MS in statistic, university of Georgia
takada_Seiya @Takada_Seiya74
2 Followers 43 Following kagoshima Univ. Orthopedic Surgery. Specially Appointed Assistant Professor. Ph.D. of Health Sciences. Physical Therapist.
Steve Lianoglou @sonuvalianos
373 Followers 3K Following Improving human health with a keyboard. Creator of https://t.co/75sw7D1WGD: modular & interactive analysis tools for genomics in #rstats. Ghana #RPCV. Amateur Dad.
Ao Huang @AoHuang2355
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br @6U39XPIiWJRAr0Y
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Kallol Datta @kdbiostat
6 Followers 246 Following PhD Research Scholar @FollowDbtNibmg Statistical Genetics and Biostatistics MSc Statistics @IITKanpur
Miguel Ángel Toro @miguel_toro0305
118 Followers 409 Following
Lior Pachter @lpachter
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Cecilia Lindgren @ceclindgren
8K Followers 1K Following Director of Oxford Big Data Institute. Proud mom of 3. Co-chair of @icdabio. Wellcome Trust Investigator. Promoting equality in academia. Love 🦈. #🕷🕸💙
Michael Love @mikelove
18K Followers 5K Following I'm not on twitter anymore, find my on Bluesky or Mastodon
Vince Buffalo @vsbuffalo
15K Followers 2K Following Evolutionary genetics postdoc @UCBerkeley ♥s biology, running, probability+statistics, 🦀, fly fishing, backpacking. Author of book Bioinformatics Data Skills
Michael 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/CvupKNIjZr
Graham 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/R6I2dcaEGf
Manolis Kellis @manoliskellis
25K Followers 4K Following Dissecting disease mechanism. Single-cell, Epigenomics, Regulatory Genomics, Disease Genetics, Brain, Cancer, Metabolism. @MIT Prof, @MIT_CSAIL, @BroadInstitute
Daniela Witten @daniela_witten
49K Followers 754 Following dorothy gilford endowed chair and prof of stat/biostat @uw. all views my own.
Dmitri Petrov 💔 @PetrovADmitri
15K Followers 4K Following Evolutionary Biologist at Stanford. Rapid Evolution, Adaptation, and Genomics. Open Science advocate.
Arjun Raj @arjunrajlab
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Yoav Gilad @Y_Gilad
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Mike Inouye @minouye271
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Alexander Strudwick Y.. @AlexTISYoung
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Bhramar Mukherjee @BhramarBioStat
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dana_peer @dana_peer
13K Followers 164 Following
Ran Blekhman @blekhman
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Wolfgang Huber 🇺�.. @wolfgangkhuber
10K Followers 1K Following Scientist working on statistical methods and applications in biology. Find me at @wkhuber.bsky.social @[email protected] Слава Україні
Alicia Oshlack @AliciaOshlack
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Ryan McShane, Ph.D. (.. @math_mcshane
84 Followers 54 Following Asst. Inst. Professor, University of Chicago Researching intransitivity in paired comparisons, (pedagogy in) sports analytics (courses). #GSG 🏀 🇩🇪 🇺🇸
Inspector Jim Jones B.. @InsJimJones
11K Followers 10K Following @gmpolice Manchester Airport Section Operations Inspector & Tactical Lead for the Armed Forces Covenant. Also a huge fan of Gibraltar. Views are my own
Richard McElreath �.. @rlmcelreath
46K Followers 2K Following Anthropologist @MPI_EVA_Leipzig - telling anyone who will listen that, if we are very careful and try very hard, we might not completely mislead ourselves
Tim Vieira @xtimv
4K Followers 1K Following machine learning, reinforcement learning, programming languages, handstands (he/him)
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Karl Rohe @karlrohe
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Orli Bahcall @obahcall
9K Followers 2K Following Editor-in-Chief @CellGenomics. Formerly Senior Editor @Nature for Genetics & Genomics, @NatureGenet @NatureRevGenet. Open science, transparency, open access.
Nicole Soranzo @nicolesoranzo
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Dr. Laura M. Huckins @LauraHuckins
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Saikat Banerjee @banskt
201 Followers 157 Following Postdoc @UChicago @HGEN_UChicago. Physicist turned bioinformatician. Current interests #eQTL, #GWAS, #genomics, #ai, #PrecisonMedicine, #ML
Yuxin Zou @zou_yuxin
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Tim Harford @TimHarford
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Peter Carbonetto @CarbonettoPeter
70 Followers 80 Following Computational Staff Scientist at Research Computing Center & Dept. of Human Genetics, University of Chicago
Cell Genomics @CellGenomics
8K Followers 926 Following Cell Genomics is a new gold #OpenAccess and #OpenScience research journal that represents the forefront of #genetics and #genomics 🧬
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259 Followers 151 Following Assistant professor of statistics @Wharton, PhD @Stanford. Seeking to unravel the mysteries of #genomics and human disease with #statistics.
Joelle Mbatchou @joellembatchou
379 Followers 264 Following Statistician. Avid book reader, world traveler and cook (recipes are welcome).
Clint Smith @ClintSmithIII
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jeremy freeman @thefreemanlab
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Mayor Muriel Bowser @MayorBowser
207K Followers 775 Following Official account of the Mayor of Washington, DC. Together, let's work to give every Washingtonian a #FairShot.
Governor JB Pritzker @GovPritzker
270K Followers 243 Following Husband and father. Proudly serving as Illinois’ 43rd governor.
Archived: Mayor Lori .. @mayorlightfoot
258K Followers 280 Following This account has been archived. For City Hall updates, follow @ChicagosMayor. For City updates, follow @Chicago.
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Valentine Svensson @vallens
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Kieran Campbell @kieranrcampbell
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Mengjie Chen @MengjieChen6
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Alexander D'Amour (al.. @alexdamour
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Sander Greenland @Lester_Domes
4K Followers 4 Following
Philip Dawid @PhilDawid
586 Followers 65 Following Emeritus Professor of Statistics in the University of Cambridge
Berk Ustun @berkustun
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Jürgen Schmidhuber @SchmidhuberAI
107K Followers 0 Following Invented principles of meta-learning (1987), GANs (1990), Transformers (1991), very deep learning (1991), etc. Our AI is used many billions of times every day.
Stanisław Jastrzębs.. @kudkudakpl
1K Followers 876 Following AI for autonomous scientific discovery. Foundations of DL (post-doc at NYU, PhD at GMUM/UoE). CTO 👨💻 & CS 🧪@ https://t.co/qJUKvd31g0. Area Chair at ICLR24.
Matt Ploenzke @MPloenzke
463 Followers 38 Following Director R&D @49ers | PhD @Harvard | Formerly RA @NYFedResearch | Alumnus @UMDBulldogs | views are my own@molly_przew @mstephens999 Congrats to @mstephens999. Well deserved!
@molly_przew @mstephens999 Yes, big congrats to @mstephens999 - and also to Elizabeth Thompson whose membership was much overdue.
@molly_przew @jcbarret @mstephens999 Congratulations @mstephens999 !! The legend grows.
Very well deserved @mstephens999 ! I’m delighted for you.
Congratulations to @mstephens999, a wonderful colleague, and now a Royal Society Fellow... royalsociety.org/news/2023/05/n…
@molly_przew @mstephens999 Wonderful news!! Congratulations Matthew!!
Congratulations to @mstephens999, a wonderful colleague, and now a Royal Society Fellow... royalsociety.org/news/2023/05/n…
@amychozick This is truly shameful whitewashing - she is a fraud and a criminal. Why are you doing this?
@SimingZhao06 @mstephens999 Amazing! It’s a very intuitive way for confounder adjustment
@mstephens999 We’ve been running MRLocus on multi-signal genes using eQTL studies in the thousands and you pick up a lot more candidates, familiar gene names popping up
"Poisson-mash", or how to detect gene expression differences in multi-condition experiments (from the group of @mstephens999, together with Nicolas Chevrier and colleagues). arxiv.org/pdf/2210.00697…
@lpachter @mstephens999 It is also a less known French fusion reconstruction of the fish and chips.
@leomrtns @mstephens999 Cod mashed in with potatoes, i.e. Poisson-mash, is quite popular in Iceland.
@lpachter @mstephens999 I was working in the lab, late one night When my eyes beheld an eerie sight For my data from his slab, around zero began to rise And suddenly to my surprise He did the Poisson-mash (The Poisson-mash)
@jmuiuc @mstephens999 I have serious issues with the NIH's ability to review computational grants. Outside GCAT, its a random disaster, and even at GCAT I find computational grant reviews severely flawed. I think I have a pretty good scientific track record and only got a single R01 in my career.
@dana_peer @Alfons_Valencia @jmuiuc @mstephens999 NIH needs a better Pe’er review system, or so it would appear
@ScienceScottT @atulbutte @jmuiuc @mstephens999 It happens with papers too, but is worse for grants, which have more rigid thinking in reviews. With papers, you need to include text to at least explain to each side why the other side is important. The path of an interdisciplinary scientist is not easy, but thrilling
@CMastication I don't like "multimodal" because an exponential mixture is unimodal. I'd call it a "mixture distribution." As physical chemists measuring quantum dot fluorescence, this functional form came up a lot and we just called it "multi-exponential."
Happy to announce that I have been promoted to Associate Professor in the Department of Biostatistics @uncbiostat and the Department of Genetics at UNC Chapel Hill. I'm grateful to the fantastic students & postdocs I've worked with here, and to my collaborators across campus.
@lcolladotor Yes, I think the power of mash modeling for eQTL is the next phase for this kind of analysis, especially for single cell.
Methods: identify cell types, pseudo-bulk, then use #mashR stephenslab.github.io/mashr by Stephens @mstephens999's lab I saw #mashR used in another #BoG22 QTL poster (I forgot the number, sorry!). We should look at it @LIBDrstats ;) doi.org/10.1038/s41588…
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