Alec Plotkin @alecplot
Bioinformatics and Computational Biology at UNC Single-cell, T-cells, and Trajectory Inference Chapel Hill, NC Joined August 2019-
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I've been reading up on flow matching recently, especially wrt. single-cell data. It seems like it's basically fitting a generative model on top of optimal transport--can anybody tell me if my intuition is right?
.@JoleneRanek @natstann @purvislab @CompMedUNC present DELVE, an unsupervised feature selection method to identify core molecular features driving cell fate decisions. #BiotechNatureComms nature.com/articles/s4146…
And now congrats to Dr. Haidong Yi for great contributions to featurizing single cell data to predict outcomes :) congratulations @haidyi1 🎉🍾🥳
Are you puzzled about your batch correction practices after reading: biorxiv.org/content/10.110… . We were too and provide some insights here. @pmelsted @adamgayoso @YosefLab @martin_kim0 colab.research.google.com/drive/15k5kahl…
In this preprint biorxiv.org/content/10.110… with @Sindri_e we compared seven widely used methods for batch correction of single cell RNA-seq data. We found that all but one of the methods introduce batch effects when there are none. 1/N
.@DylanLSchaff et al. show that resistant cancer cell clones are different from one another, yet the cells within a clone remain similar during treatment. Transcriptional differences between clones result in different cell fates when treated sequentially with different agents or…
Very evocative figure. "We present an alternative to Graph Neural Networks (GNNs) termed Graph Structured Neural Networks (GSNN), which uses cell signaling knowledge, encoded as a graph data structure, to add inductive biases to deep learning."
Congratulations @alecplot for winning a best poster award at data science day for work predicting CD8 T-cell fates with @JJMilnerLab :) Truthfully, this a picture from last week, but is the same poster. Great job Alec.
So you just used a fancy deep-learning method (e.g., U-Net) to segment your cells. Do you trust your results? Should theorists model your data? Beware of “What You Put Is What You Get (WYPIWYG).” Your results will reflect your bias in your training dataset. Short thread. 1/
Interested in "integrating" multimodal #scRNAseq data? W/ @MariaCarilli, @GorinGennady, @funion10 & Tara Chari we introduce biVI, which combines the scVI variational autoencoder with biophysically motivated bivariate models for RNA distributions. 🧵 1/ biorxiv.org/content/10.110…
Just found out that python's default behavior is to prioritize loading packages in your base installation over your active conda environment... that was a fun bug to fix 🥲
Scientists spend too much time taking “professional selfies”. A paper from PNAS describes what it takes to be a scientist today. Key points (that I always emphasize myself): #AcademicTwitter @AcademicChatter #research
How to stay on top of the literature? Here are 5 tips to stay current, just follow along ⬇️
Do you want to get into scRNA-seq but are lost in the sea of never-ending papers? No worries, I got you covered. Here's a list of the best review that have help me understand the core concepts of the technique, analysis and interpretation:🧵
Do you want to get into scRNA-seq but are lost in the sea of never-ending papers? No worries, I got you covered. Here's a list of the best review that have help me understand the core concepts of the technique, analysis and interpretation:🧵
Congratulations to Chi-Jane who led our new paper on graph coarsening approaches for single-cell data. We show that by shrinking the graph in a principled way, you can achieve similar performance in downstream bioinf tasks as if using the full graph. biorxiv.org/content/10.110…
Great initiative. As someone who uses scanpy often, I'm excited to see what comes out of this!
Great initiative. As someone who uses scanpy often, I'm excited to see what comes out of this!
me writing SLURM jobs vs. me debugging SLURM jobs
does anyone else get anxiety after submitting a SLURM job?
Today is the last day of @alecplot ‘a rotation with us and @JJMilnerLab . He did a great job and is on the way to becoming both an expert of T-cells and graphs. What a great combo of content 🧫👨💻 :) thanks for joining us Alec!
"Ontogeny of plasma cytokine & chemokine concentrations across the 1st week of human life" published in @ElsevierConnect #Cytokine. This work, from the @PrecVaccines EPIC@hipcProject, will help future studies better understand the neonatal immune system. bit.ly/3iwV9Wl
GwendolynFord @Y5mIlHYeY73eS4W
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Will Townes @will_townes
2K Followers 2K Following Asst Prof @CMU_StatDS interested in infectious disease (@CMUDelphi), genomics, time series, and discrete stable distributions. https://t.co/DKllr8Ffzm
William Green @greenwilliamd
78 Followers 254 Following Nutrition | Immunology | Metabolism | UNC-Chapel Hill | Former Davidson Wildcat
Jess Byun @Jess_S_Byun
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Hadden @kanmonmaya10075
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Sarah Parker @SarahInSilico
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Danielle Szafir @dalbersszafir
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Brandon Pratt @Pratt__Brandon
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UNC School of Data Sc... @UNCSDSS
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Gang Li @FrankLeeGangLi
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Dilara A. @codingdilara
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bubble-inza @Shopkins9696
505 Followers 4K Following stop sending me stuff of private parts people-just because I love seeing them in drawings doesn't mean I love seeing them on media so stop it you morons
Jonah Librach @jonahlibrach
772 Followers 4K Following AI-powered figure creation for blots, gels and microscopy
Jin Seok (Andy) Lee @iam_js_lee
176 Followers 490 Following PhD candidate in bioinformatics & computational biology @pirl_unc | Long-read sequencing | Neoantigen discovery
Dan Schrider @SamurSciCop
1K Followers 736 Following An aquatic ape studying population genetics at the University of North Carolina.
North Carolina Biotec... @NCBionetworks
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Benjamin McMichael @Benjamin_McM
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Le (Lena) Huang @LeHuang9
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Josh Sikder @JoshS_v2
49 Followers 119 Following Former member @SamurSciCop lab. Evolutionary biology and phylogenetics. Sushi Go certified.
Kate @dontpanickid
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Geo Fox @WillClone4Food
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amrita @amrita_nal
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Christoph Rau @The_DataDragon
143 Followers 167 Following Assistant Professor of Computational Medicine at UNC-Chapel Hill. Interested in good discussions and collaborations! Other: @christophrau.bsky.social
Amy @aponteamy
159 Followers 296 Following PhD candidate in Pharmacology | Dr. Mike Emanuele’s Lab at UNC-CH 🧬
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100 Followers 180 Following GMB PhD candidate at the University of North Carolina at Chapel Hill. Member of the Jean Cook Lab. Penn State University B.S. '17. Tweets and views are my own
Alyssa Edwards @alys_edward
45 Followers 139 Following UNC-Chapel Hill BBSP PhD Student 🧬🥼 | Ramsden Lab
Matt Regner (he/him) @RegnerMJ
235 Followers 502 Following PhD Candidate at UNC Chapel Hill | #singlecell & #compbio | https://t.co/oEPUqd2BP8
UNCShadowAScientist @Shadow_UNC
142 Followers 148 Following Connecting research scientists with the community. Get involved! https://t.co/M2Z5R3OGLh
Kwame Forbes @kwame_forbes
81 Followers 111 Following I’ll let you know after my first year of graduate school @ UNC Chapel Hill
Olivia Steiner @oliviasteiner28
82 Followers 166 Following PhD Student @UNCBBSP @UNCChemistry | @Tufts 2021
Christina @minjunoooo
103 Followers 245 Following PhD student of Neher Lab with an unhealthy dose of non-science tweets
Gilbert Giri @GilbertGiri2
199 Followers 483 Following Pre-doctoral trainee @UNCBBSP @UNC | @UofR Class of 21
Reagan Bullins @ReaganBullins
177 Followers 272 Following Neuroscience PhD Candidate in @AdamHantman Lab @UNC_SOM interested in motor cortical dynamics • @Shadow_UNC content creator 🎥 • alum @VTNeuro
Dr. Jamshaid A. Shahi... @jamshaid_shahir
420 Followers 801 Following Computational Biologist | UNC PhD '23 🧬 | @UMBC '18 | Towards Data Science Writer 💻 | Cat Dad 🐈⬛ | Tea Drinker ☕️ | Science Communicator🔬
Haeun (Hannah) Hwangb... @HaeunHwangbo
64 Followers 57 Following Bioinformatics & Computational Graduate Student at UNC-Chapel Hill
Sool Lee, PhD @will_s_lee
60 Followers 119 Following Migrating to bluesky https://t.co/zwWLFWgPuf 🧬 Ph.D Bioinformatics and Computational Biology | Dog Dad | All views are my own
Kinga Smolen @KingaSmolen
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Dr. Amy Pomeroy @AmyEPomeroy
268 Followers 441 Following Computational Cancer Pharmacologist | Postdoctoral Researcher at UNC Chapel Hill
Alex Neary @AlexNeary25
50 Followers 47 Following Family, Friends, and Science — @UNCBBSP Biophys PhD student
The Biologist @thebiologist14
3K Followers 4K Following A Platform Exclusively For Life Science Researchers.
Danial Babaki @Danielbbki
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Computational Bioscie... @compbiosci_unc
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BBSP @ UNC @UNCBBSP
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nyssa tucker @n_tuckity
261 Followers 2K Following Natural philosopher / health scientist | they/they
Eric Sun @EricDSun
949 Followers 210 Following Machine learning for aging, spatial/single-cell omics, immunology || Incoming Assistant Professor @MIT | PhD @Stanford
Nature Reviews Bioeng... @natrevbioeng
4K Followers 180 Following A new online-only journal from @NaturePortfolio publishing high-quality Reviews, Perspectives and Comments across all areas of bioengineering.
Joe Pickrell @joe_pickrell
14K Followers 1K Following Geneticist, entrepreneur. Co-founder and Board @gencove. Current projects: @getcrimsoniris, TBD
Yann LeCun @ylecun
954K Followers 765 Following Professor at NYU. Chief AI Scientist at Meta. Researcher in AI, Machine Learning, Robotics, etc. ACM Turing Award Laureate.
Michael Bronstein @mmbronstein
54K Followers 6K Following #DeepMind Professor of #AI @UniofOxford / Director #AITHYRA / Chief Scientist @vant_ai / https://t.co/kZpGpDzYeV (opinions are mine) 🤖🧪🧬🎶🐎
Katarina Petrovic @kpetrovvic
834 Followers 285 Following PhD Student in ML at @UniofOxford 👩🏻🔬 with @mmbronstein and @ismaililkanc focusing on Generative AI 🤖 + bio 🧬
Lazar Atanackovic @lazar_atan
617 Followers 993 Following Incoming Assistant Professor @UAlberta. Fellow @AmiiThinks. Currently, postdoc fellow @broadinstitute @Schmidt_Center. Views my own.
Biology+AI Daily @BiologyAIDaily
14K Followers 266 Following Protein/Antibody Designer, AI for drug design, Deep learning and large language model. Share daily papers on biology + AI
Recursion @RecursionPharma
15K Followers 773 Following Decoding biology to radically improve lives. The industrial revolution of drug discovery is here.
Jeff Sekelsky @mei_newt
1K Followers 545 Following Mentor & sarcastic geneticist @UNC; I ♥️chromosomes. Card-carrying member of ACLU and Genetics Society of America. Green Bay Packers owner. he/him/his
Josh Sikder @JoshS_v2
49 Followers 119 Following Former member @SamurSciCop lab. Evolutionary biology and phylogenetics. Sushi Go certified.
Uri Alon @UriAlonWeizmann
11K Followers 497 Following Now on Bluesky @urialonlab.bsky.social The Alon lab explores design principles of biological circuits, focusing on systems medicine, ageing and healthspan.
Asimov Press @AsimovPress
9K Followers 131 Following Asimov Press is a publisher focused on the science and technologies that promote flourishing. Part of @AsimovBio. Supported by @AsteraInstitute and @Stripe.
ISCB News @iscb
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Eric Kernfeld @ekernf01
1K Followers 2K Following Statistician and computational biologist; alum @maehrlab, @cahanlab, @alexisjbattle lab. Views are not those of my employer. He/him. https://t.co/jaMuFiHjk0
Itai Yanai @ItaiYanai
32K Followers 2K Following Professor at the NYU School of Medicine. Co-host of the 'Night Science Podcast' @nightsciencepod and Co-founder of the Night Science Institute https://t.co/lede3rBmXU
Jian Ma @jmuiuc
8K Followers 1K Following Ray and Stephanie Lane Professor of Computational Biology at CMU School of Computer Science @CMUCompBio @SCSatCMU @CarnegieMellon
Dan Roy @roydanroy
57K Followers 2K Following ML / AI researcher. Research Director and Canada CIFAR AI Chair, @VectorInst. Professor, @UofT (Statistics/CS).
NimwegenLab @NimwegenLab
4K Followers 179 Following Gene regulatory networks and genome evolution. How do single cells make up their minds? @[email protected]
Niko McCarty. @NikoMcCarty
41K Followers 1K Following Science. Biology. Progress. Founding Editor @AsimovPress / Subscribe!
Alex Wolf @falexwolf
2K Followers 377 Following Open data infra for biology @laminlabs. Previously, created Scanpy & led build-up of Cellarity's compute platform.
Fabian Theis @fabian_theis
35K Followers 424 Following Computational biologist @HelmholtzMunich, prof @TU_Muenchen & associate PI @sangerinstitute. Dad of 4 and mountain lover. Department news, see @CompHealthMuc
Juhyun Kim @juhyunk_
1K Followers 451 Following Ph.D | Seoul National Univ ‘19 | Genomic Medicine Institute(GMI) | scRNA-seq, multiomics, Spatial genomics, sceQTL, GWAS, and Human reference 🧬
Ben Schmidt / @benmsc... @benmschmidt
9K Followers 1K Following VP of Information Design @nomic_ai, building new ways to interpret and shape embedding models. Onetime history/digital humanities prof. @bschmidt.bsky.social
Dmitry Kobak @hippopedoid
8K Followers 235 Following Researcher at @uni_tue. Manifold learning, contrastive learning, scRNAseq data. Excess mortality. Born but to die and reas'ning but to err.
Jack Morris @jxmnop
46K Followers 988 Following research @cornell // language models, information theory, science of AI
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151K Followers 1K Following Nature Methods publishes cutting-edge methods, tools, analyses, resources, reviews, news and commentary, supporting life sciences research. Tweets by editors.
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Yosef Lab @YosefLab
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Patrick Schwab @schwabpa
7K Followers 2K Following ML for Drug Discovery and Health. Posts are personal opinions.
North Carolina Biotec... @NCBionetworks
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Can Ergen @_canergen
222 Followers 152 Following Postdoc at @UCBerkeley and @UCSF. Co-mentored by @Yoseflab and @yimmieg
ElowitzLab @ElowitzLab
12K Followers 1K Following Lab of Michael Elowitz at Caltech. Synthetic biology and systems biology
Nick Haining @nickhaining
3K Followers 1K Following CSO and co-founder of @ArsenalBio via @DanaFarber, @broadinstitute, and @Merck. He/his.
Bo Wang @BoWang87
13K Followers 2K Following SVP and Head of Biomedical AI @Xaira_Thera; Associate Prof @UofT; Chief AI Officer @UHN; former PHD, CS @Stanford; opinions my own. #AI #healthcare #biology
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Dr. Stacey Finley (US... @USCSysBio_Lab
3K Followers 1K Following Developing mathematical models to better understand biochemical networks and identify drug therapies. Directed by Dr. Stacey Finley, Professor of BME @USC
Cell Systems @CellSystemsCP
7K Followers 511 Following A monthly, peer-reviewed journal from Cell Press devoted to Systems Biology. Posts from the Editors. We are on Bluesky @cp-cellsystems.bsky.social
Brandon Pratt @Pratt__Brandon
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