Lior Pachter @lpachter
Bren Professor of Computational Biology @caltech. Blog at https://t.co/FFQzhEsmhi. Tweets represent my views, not my employer's. #methodsmatter pachterlab.github.io Pasadena, CA Joined April 2009-
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A funny thing happened on the way to routine single nucleus ATAC-seq analysis…and after scratching at it for longer than we wanted, we wrote a paper about what we found. This is a 🧵 about our little paper...(sorry long) biorxiv.org/content/10.110… 1/
Inspired by @lpachter and team's exploration of scRNA-seq pipelines, we face similar challenges in scATAC-seq, only magnified! After 5 years of tackling these inconsistencies with my advisor @JunhyongKim , Here is a summary (and some solutions😃) 1/n #Genomics #Bioinformatics
Inspired by @lpachter and team's exploration of scRNA-seq pipelines, we face similar challenges in scATAC-seq, only magnified! After 5 years of tackling these inconsistencies with my advisor @JunhyongKim , Here is a summary (and some solutions😃) 1/n #Genomics #Bioinformatics
So, seqspec has been published. This is a good opportunity to remind everybody that your count matrix, R object, h5ad etc are NOT your raw data. Raw data are fastq files which are only useful when you know the content of your reads. Then ... 1/7 academic.oup.com/bioinformatics…
@MCATstudySesh @NatureMicrobiol Thank you, and you are absolutely right. We can now integrate decades of data on chemotaxis, and this comprehensive understanding opens up numerous exciting avenues. I have discussed some of these in a 'Behind the Paper' blog post here: go.nature.com/3xLFcWr
(1/3) Excited to share our newest publication!! Fun collaboration with the Chen and Severinov labs to investigate how the fluoride riboswitch rearranges a pseudoknot to form a terminator. See movie generated by @elisew00 and Alan Chen (@TheRNAInstitute) academic.oup.com/nar/article/do…
In order to further the development of an open database of scientific illustrations for the life sciences we have now set up a non-profit under the umbrella of @OC_Europe 1/ opencollective.com/bioicons
Our paper "A machine readable specification for genomics assays" is now published in Bioinformatics, @OUPBioinfo. In short, we present a lightweight file format and command-line tool to document the structure of sequencing reads. Coauthored with @XiChenUoM and @lpachter. Paper:…
I am shocked to learn that @NCBI has no documentation on the SRA file format. An example of good transparency (the source code is available) but poor usability (a major barrier to building tools to work directly with SRA files). github.com/ncbi/sra-tools…
I am shocked to learn that @NCBI has no documentation on the SRA file format. An example of good transparency (the source code is available) but poor usability (a major barrier to building tools to work directly with SRA files). github.com/ncbi/sra-tools… https://t.co/ef5ORN8lF5
@lpachter p values are for getting tenure, not figuring out truth.
@eilatg Lots of good wave suggestions. I recommend James’s “A Student's Guide to Fourier Transforms” as a super clear intro to Fourier methods. Winning opener: “Showing a Fourier transform to a physics student generally produces the same reaction as showing a crucifix to Count Dracula.”
We have a winner! The plot has R^2 = 0.0067. p = 0.01. @leonidmirny guessed R^2 = 0.01, p = 0.01. Spot on! I made this plot by writing a program to find examples by shifting initially random points towards a line close to 0 (similar to the datasaurus approach).
We have a winner! The plot has R^2 = 0.0067. p = 0.01. @leonidmirny guessed R^2 = 0.01, p = 0.01. Spot on! I made this plot by writing a program to find examples by shifting initially random points towards a line close to 0 (similar to the datasaurus approach).
I've noticed it's becoming increasingly common in genomics to report results of regressions with ridiculously low correlation as "significant" based on a tiny p-value (for the hypothesis that the slope = 0). Can you guess R^2, the p-value, and where the data below was published?
Another paper on utility of polygenic risk scores: nature.com/articles/s4146… tl;dr: polygenic risk scores have no utility.
A not so tacit acknowledgment that "the Human Cell Atlas [project has]... failed" 👀
A not so tacit acknowledgment that "the Human Cell Atlas [project has]... failed" 👀
@lpachter Fun fact: Vampire bat oronasal-expressed isoform of TRPV1 (ortholog to our heat/pain/capsaicin receptor) melt-refolds at ~temperature of cool night/air close to another living mammal... Basically, their victims smell/taste spicy-hot good to them.
"A correlation coefficient of > 0.1 was used as the criterion of a validated model" That's r^2 = 0.01 👀
Startup idea: mine the ghost proteome in vampire bats, specifically looking for homologs of the Arabidopsis WEREWOLF gene (in order to unlock the secrets of longevity in humans).
Ugh. Yet another confirmation that the tool used to preprocess single-cell RNA-seq really matters. In this case a comparison of some split-seq quantification tools. Ugh. bmcgenomics.biomedcentral.com/articles/10.11…
I saw the chicken crossing the road in Pasadena yesterday but I don't know why it chose to do so.
Fabian Theis @fabian_theis
29K Followers 445 Following Computational biologist @HelmholtzMunich, prof @TU_Muenchen & associate PI @sangerinstitute. Dad of 4 and mountain lover. Department news, see @CompHealthMuc
Itai Yanai 💔 @ItaiYanai
23K Followers 2K Following Professor at the NYU School of Medicine. Co-host of the 'Night Science Podcast' https://t.co/Sy1rcWXGLz @nightsciencepod
Anshul Kundaje (anshu.. @anshulkundaje
22K Followers 2K Following Genomics, Machine Learning, Statistics, Big Data and Football (Soccer, GGMU). Post: @anshulkundaje, Threads: anshulkundaje
Arjun Raj @arjunrajlab
25K Followers 2K Following Just another LLM. Tweets do not necessarily reflect the views of people in my lab or even my own views last week. https://t.co/fZAnUCqd12
Prof. Nikolai Slavov @slavov_n
14K Followers 264 Following Mentor, scientist & engineer. Director of @ParallelSqTech. Having fun in @SlavovLab with single-cell proteomics & ribosomes. Organizer of @SCP_meeting
dana_peer @dana_peer
13K Followers 164 Following
Ewan Birney @ewanbirney
50K Followers 2K Following Deputy Director General of EMBL, Director of EMBL-EBI. I have an insatiable love of biology. @[email protected]. I also work with ONT, Dovetail + GeL.
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
Mick 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.
Simona Cristea @simocristea
7K Followers 496 Following Head of Data Science at Hale Center for Pancreatic Cancer | Group leader @DanaFarber @Harvard | We ❤️ genomics, evolution & LLMs | PhD @eth | 🇷🇴🇸🇪🇨🇭🇺🇸
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
Luciano Martelotto �.. @LGMartelotto
10K Followers 953 Following Sc/St-Omics pro-aficionado. Knowledge sharing is my thing. Views, opinions and comments are my own and do not represent those of my employer. Like/RT ≠ endorse
Heng Li @lh3lh3
10K Followers 207 Following Associate professor of biomedical informatics at @HarvardDBMI and @dfcidatascience
Aaron Quinlan @aaronquinlan
17K Followers 1K Following Genome mutation, software for genomic discovery. https://t.co/6GKjALLFfk Co-director, DELPHI Data Science Init.: https://t.co/8uWRcIzWRr
Joshua 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 bills
Mo Lotfollahi @mo_lotfollahi
6K Followers 1K Following I train neural networks and dogs to do cool things! ML for biology and drug discovery| Faculty @sangerinstitute.
Jian Ma @jmuiuc
7K Followers 1K Following Ray and Stephanie Lane Professor of Computational Biology at CMU School of Computer Science @CMUCompBio @SCSatCMU @CarnegieMellon
Jason Sheltzer @JSheltzer
17K Followers 2K Following Assistant prof at @YaleMed. Interested in aneuploidy, mitotic kinases, drug targeting, CRISPR, and promoting diversity in science. Co-founder @MelioraTx.
Dan Landau @landau_lab
9K Followers 2K Following Cancer genomics, epigenomics and evolutionary dynamics (Weill Cornell/New York Genome Center). Hemato-oncologist (NYP). Discl.: https://t.co/tAu87FMVW3
PrrrSchKa @PrrrSchKa
0 Followers 804 Following
Prof @MaxmanGomo
1K Followers 4K Following MSc Agric Animal Science| Animal Breeding and Genetics| Quantitative Genetics|DNA profiling|Parantage verification|Genomics
Thahmina Ali @ThahminaAli
1 Followers 25 Following
Martin Njau Kamau @MartinNjauKama2
2 Followers 59 Following
Arjun Ramakrishnan @cognoman5
1K Followers 819 Following Assistant Professor, Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur. Co-founder of Cogwear Technologies, LLC Philadelphia, USA
Aartik Sarma @AartikSarma
724 Followers 597 Following Physician-scientist @UCSF PCCM and affiliate faculty @UCJointCPH • Precision medicine in ARDS, COPD, and sepsis 🖥️🧬🫁🦠
Sara Ghaffari @saragh.. @saraghaffari8
642 Followers 4K Following Ph.D (UTM), Editorial Board Member (emerald PUBLISHING), Founder, Child Development, Primate Behaviours, Conservation, Occasionally a Poet @saraghaffari7
Guillermo VillOlea @villagomezolea
377 Followers 279 Following PhD student at @KingsCollegeLon, Centre for Craniofacial and Regenerative Biology. #Latinx Mis alma maters @UNAM_MX @BUAPOficial
fangnong lai @FangnongL
46 Followers 752 Following
Mathematical Bioscien.. @MBS_Journal
0 Followers 131 Following Tweets from the journal "Mathematical Biosciences" - insights and info from the editors!
Maxime Meylan @MaximeMeylan
319 Followers 280 Following Research fellow at the Dana-Farber Cancer Institute and Harvard Medical School. Computational immunology / Spatial transcriptomics
Jack Tan @JyeJack
32 Followers 125 Following Passionate about genomics and science transforming our world into a better place. Views expressed are my own.
Quim Martí @QMartiB
151 Followers 1K Following Biomedical engineer interested in cancer modelling and synthetic biology
Lorenzo Martini @LorenzoGAGAM
4 Followers 20 Following Phd. researcher at Politecnico di Torino - bioinformatic, computational biology, genomics - currently interested in transcriptional regulation!
Bing Shui @shui_bing
138 Followers 276 Following Interested in cancer and regeneration. current postdoc @LabJacks. PhD @BBS_Harvard and @KevinHaigisLab. BA @CarletonCollege
Jordan Taylor @jtaylor_tweets
119 Followers 260 Following PhD student @EdinburghUni. Was a PVDF surgeon, turning into a something else.
Ana M. Florez-Rueda @AnaM_FlorezR
183 Followers 333 Following Plant Scientist – Humboldt Fellow 🇨🇴 | @MPIMP_Potsdam @unipotsdam 🇩🇪| Evolution | Development | Genomics 🌿🌺
Dan Okin @danokin
363 Followers 437 Following Physician Scientist @HarvardPulm @MGHmedicine | Post-doc in @jkagan1 lab | @RMedzhitov alum | Immunology and evolutionary biology
Michael Adeniya @michaeladeniya
752 Followers 2K Following MD at @FoGenomics . Husband. Father.📍Newport. Made in🇳🇬
Matt Stergiou @MattStergiou
818 Followers 2K Following Data & AI @TempusLabs. DM me to join our 70+ member monthly nyc biotech run club. @bitsinbio NYC @LBF_org Cohort 1 🇨🇦 in 🇺🇸
Peter C. Allen @PeterAllen225
246 Followers 475 Following Postdoctoral Researcher in the @drjosephpowell lab at @GarvanInstitute using sc-omics to understand various ILDs | @crepulmfibrosis Fellow | Views are my own
Cameron Stow @camerontstow
855 Followers 1K Following Startup Community & Marketing Manager | AI, Web3, DeSci, HealthTech | @_Alphalyst
Yifei Weng @Yifei83155584
80 Followers 214 Following Grad Student from Murphy Lab @ctmurphy1 at @Princeton. Loves neurons, genomics, C. elegans, and of course aging
Lumbani @Rulingz
54 Followers 604 Following
Vincent @VincentBouget
51 Followers 146 Following
Anna Nordin @AnnaNordin96
103 Followers 120 Following PhD student in the Cantù lab studying Wnt signaling and chromatin structure during development and disease
Lucas Kampman @LucasKampman
15 Followers 72 Following Incoming class of '23, UW/Fred Hutch MCB PhD. Past: Corces Lab @GladstoneInst, Laura Kaufman Group @ChemColumbia, Hallatschek Lab @BerkeleyPhysics
Akash Nagarajan @AkashRhaegar
125 Followers 244 Following PhD research @UABNews | science & tech dev history buff | #aging #neuroscience #epigenetics
Helena Lucia Crowell @helucro
437 Followers 124 Following postdoc @hoheyn lab @cnag_eu 🇪🇸 • 🇺🇸🇬🇷🇩🇪 sports fanatic. avid reader. nature lover. travel addict. wannabe pianist. science enthusiast.
Boltzmann Labs @LabsBoltzmann
50 Followers 178 Following A Company with the vision of revolutionizing Drug Discovery. Designing precision medicine with data-driven solutions.
Ludwig Erlmeier @LudwigErlmeier
1 Followers 2 Following
Alyssa Baccarella @abacc22
71 Followers 244 Following Pediatric gastroenterology fellow at CHOP. Interested in how we can use transcriptomics to better understand the immunology of IBD.
Jorge Bastos @thisisjbastos
34 Followers 220 Following 'Every kid starts out as a natural-born scientist, and then we beat it out of them.' - Carl Sagan. I'm still resisting...
Guneet Singh Kohli @guneetsk99
445 Followers 3K Following AI Engineer @ GreyOrange, Building Indian LLMs with Odia GenAI Independent Researcher working on variety of random problems.
Yan Ting Ng @Nytingale19
0 Followers 3 Following
hypervanse @hypervanse
118 Followers 652 Following PhD in Physics, researcher, programmer, musical artist, gamer... 超人
Spincoater @SETCASLLC
197 Followers 2K Following Spin coater Dip coater Plasma cleaner Mask aligner lithography Sputter coater UV cleaner Hot plate Film application from SETCAS LLC in USA
Haruo Suzuki @copypasteusa
1K Followers 2K Following 慶應義塾大学。バイオインフォマティクス、ゲノム微生物学、都市のマイクロバイオーム。 Keio University. Bioinformatics, Genome Microbiology, Urban microbiomes. #MetaSUB
Joey Avenger Jr. @joyfulmath3
200 Followers 268 Following I love maths, science, art, education, history, music.
Freya Herrmann-Sim @FreyaHS2002
2 Followers 72 Following
Fabian Theis @fabian_theis
29K Followers 445 Following Computational biologist @HelmholtzMunich, prof @TU_Muenchen & associate PI @sangerinstitute. Dad of 4 and mountain lover. Department news, see @CompHealthMuc
Itai Yanai 💔 @ItaiYanai
23K Followers 2K Following Professor at the NYU School of Medicine. Co-host of the 'Night Science Podcast' https://t.co/Sy1rcWXGLz @nightsciencepod
Anshul Kundaje (anshu.. @anshulkundaje
22K Followers 2K Following Genomics, Machine Learning, Statistics, Big Data and Football (Soccer, GGMU). Post: @anshulkundaje, Threads: anshulkundaje
Arjun Raj @arjunrajlab
25K Followers 2K Following Just another LLM. Tweets do not necessarily reflect the views of people in my lab or even my own views last week. https://t.co/fZAnUCqd12
Prof. Nikolai Slavov @slavov_n
14K Followers 264 Following Mentor, scientist & engineer. Director of @ParallelSqTech. Having fun in @SlavovLab with single-cell proteomics & ribosomes. Organizer of @SCP_meeting
Ewan Birney @ewanbirney
50K Followers 2K Following Deputy Director General of EMBL, Director of EMBL-EBI. I have an insatiable love of biology. @[email protected]. I also work with ONT, Dovetail + GeL.
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
Mick 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.
Simona Cristea @simocristea
7K Followers 496 Following Head of Data Science at Hale Center for Pancreatic Cancer | Group leader @DanaFarber @Harvard | We ❤️ genomics, evolution & LLMs | PhD @eth | 🇷🇴🇸🇪🇨🇭🇺🇸
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
Luciano Martelotto �.. @LGMartelotto
10K Followers 953 Following Sc/St-Omics pro-aficionado. Knowledge sharing is my thing. Views, opinions and comments are my own and do not represent those of my employer. Like/RT ≠ endorse
Heng Li @lh3lh3
10K Followers 207 Following Associate professor of biomedical informatics at @HarvardDBMI and @dfcidatascience
Aaron Quinlan @aaronquinlan
17K Followers 1K Following Genome mutation, software for genomic discovery. https://t.co/6GKjALLFfk Co-director, DELPHI Data Science Init.: https://t.co/8uWRcIzWRr
Joshua 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 bills
Jian Ma @jmuiuc
7K Followers 1K Following Ray and Stephanie Lane Professor of Computational Biology at CMU School of Computer Science @CMUCompBio @SCSatCMU @CarnegieMellon
Dan Landau @landau_lab
9K Followers 2K Following Cancer genomics, epigenomics and evolutionary dynamics (Weill Cornell/New York Genome Center). Hemato-oncologist (NYP). Discl.: https://t.co/tAu87FMVW3
Cecilia Lindgren @ceclindgren
8K Followers 998 Following Director of Oxford Big Data Institute. Proud mom of 3. Co-chair of @icdabio. Wellcome Trust Investigator. Promoting equality in academia. Love 🦈. #🕷🕸💙
Adam Phillippy @aphillippy
18K Followers 1K Following Goodbye Twitter 👋 You can now find me on bsky. I'll also try and post research updates more frequently on my lab homepage, linked below ⬇️
Nils Homer @nilshomer
6K Followers 746 Following I write software for Biologists. Founder @fulcrumgenomics, Bioinformatician, Computer Scientist, Coder, Father of 2xGirls. Opinions are my own.
Zhen Miao @ZhenMiao2
352 Followers 265 Following PHD student, genomics & computational biology @Pennmedicine @UPenn | single cell multi-omics in human complex diseases | statistical modeling of gene regulation
Chase Brownstein @ChaseBrownstein
2K Followers 1K Following Graduate Student @yale_eeb @Yale & YC '23 Call me the ancient mariner cus I'm about to Bust a Rime https://t.co/xuvCO9jyYY he/him
Dr Valeria dePaiva @valeriadepaiva
3K Followers 2K Following Logician, category theorist, semanticist. Likes to understand life mathematically. She/Her
Alex Wolf @falexwolf
2K Followers 337 Following Open-source data tools for biology @laminlabs. Previously, created Scanpy & led build-up of Cellarity's compute platform.
Tom Gur @TomGur
4K Followers 281 Following Associate Professor of Theoretical Computer Science @Cambridge_Uni. My research is in Complexity Theory and Quantum Computing.
Richard Behringer @rrbehringer
6K Followers 47 Following Developmental biologist, geneticist, & reproductive biologist. PhD. Son of an immigrant. Hispanic Filipino American.
Ofir Lindenbaum @Ofirlin
805 Followers 2K Following Assistant professor at Bar Ilan University. Primary research is Machine learning, computational biology, and signal processing.
Björn Schumacher @schumacherbj
17K Followers 2K Following I'm a scientist 👨⚕️, author 📕and chair for genome stability in aging and disease at the University of Cologne
Zach B. Hancock @zachbbionerd
905 Followers 666 Following Evolutionary biologist. Postdoc at UMich with @gbradburd. he/him
Karsten Rippe @KarstenRippe
1K Followers 63 Following
MD BABU MIA, PHD @BabuuDx
517 Followers 99 Following #Hematology #Oncology research(14+ years) #Bioinformatician #Single cell Multiomics #MPN #Myeloma #Aging @IcahnMountSinai .Alum.@IndianaUniv
Kasper Green Larsen @kasperglarsen
1K Followers 233 Following Professor and Head of Algorithms, Data Structures and Foundations of Machine Learning at Computer Science, Aarhus University
Shreya Saxena @shreyaneuroctrl
2K Followers 1K Following Computational neuroscientist with a background in control theory. Asst Prof at Wu Tsai Institute & BME @Yale. Previously @UF. Postdoc @Columbia. PhD @MIT.
Marine Biological Lab.. @MBLScience
27K Followers 15K Following The Marine Biological Laboratory (MBL) is an international center for research & education in biology & ecology in Woods Hole, MA. An affiliate of @UChicago.
Theofanis Karaletsos @Tkaraletsos
4K Followers 2K Following Head of AI @cziscience | probabilistic and deep ML
Federico Marini - @fe.. @FedeBioinfo
1K Followers 1K Following Head of the Bioinformatics Group @ Institute of Medical Biostatistics, Epidemiology and Informatics @UnimedizinMainz, 🇮🇹 in 🇩🇪, loves 💻🧬🩸☀️🍹🌲🏖️ He/him
Arendt Lab @wormduty
2K Followers 152 Following Lab of Detlev Arendt, tweets by *any* of the lab members. Working to understand cell type evolution with the weirdest beasties we can find!
Eve Seuntjens @EveSeu.. @EveSeuntjens
948 Followers 884 Following Developmental biologist studying brain evo-devo. Cephalopodian. Based @KU_Leuven
Jonas Demeulemeester @zeunas
543 Followers 557 Following Group Leader at the VIB – KU Leuven Center for Cancer Biology @vib_ccb and @Onco_KULeuven interested in tumour evolution, single-molecule multi-omics, and AI
Jordi Solana @solana_jordi
1K Followers 1K Following SCBE lab at the Living Systems Institute, University of Exeter. Chops planarians in pieces... or in single cells.
Lauren Saunders @LSaund11
580 Followers 667 Following ✨ Brand new Junior Professor @COSHeidelberg former postdoc w/ @coletrapnell. @parichylab alum dev bio | zebrafish | neural crest | single cell genomics. she/her
Ari Kaplan @arikaplan1
4K Followers 3K Following Databricks ; Caltech Alumni of the Decade ; Moneyball analyst for MLB teams, creator of Cubs analytics dept, SMWW Baseball Faculty
Domenic Narducci @DomenicNarducci
147 Followers 405 Following PhD student in @hansen_lab interested in transcription factors and microscopy. @MIT '20. He/him 🏳️🌈
Anders Sejr Hansen @Anders_S_Hansen
4K Followers 2K Following Associate Professor @MITdeptofBE : https://t.co/uy48t7k949 Interested in understanding the relationship between 3D genome structure and function
Prof Michael E. Mann @MichaelEMann
223K Followers 2K Following Scientist/Author; Presidential Distinguished Professor/Director Center for Science, Sustainability & the Media, U Penn; Nat Academy of Sciences; Tyler Prize
zara weinberg 🧪�.. @weinberz
8K Followers 5K Following cell signaling, synbio, publication anarchist, mentoring, teaching, curiosity, caring. #NIHMOSAIC Scholar w/ @HanaScientist 🧙🏻♀️👩🏻🔬🏳️🌈⚧ she/her
Pardis Sabeti @PardisSabeti
21K Followers 373 Following Professor @harvard @HarvardChanSPH @broadinstitute using genomics to impact infectious disease. Views are my own. @sabeti_lab @1000daysband
Talya Eden @TalyaEden
40 Followers 99 Following Assistant Professor - Algorithms and TCS, Bar-Ilan University
Pieter Mestdagh @pieter_mestdagh
668 Followers 395 Following PI @ Ghent University - oncoRNAlab. Computational Biology manager @ CellCarta
Dr. Jennifer Raff @JenniferRaff
17K Followers 1K Following Anthropological genetics, martial arts, writing, ham radio, bats. NYT bestselling author and professor. Rock chalk. @jenniferraff.bsky.social
Joao Ascensao @jaascensao
181 Followers 338 Following Grad student @ UC Berkeley with @ohallats | Dynamics of microbial ecology & evolution | @[email protected]
Georgia Gkioxari @georgiagkioxari
9K Followers 412 Following Assistant professor in Computing + Mathematical Sciences @Caltech 🏛️ ∙ Computer vision enthusiast 🤖 ∙ Previously at @metaai 👩🏻💻∙ From 🇬🇷
Kostas Kampourakis @KampourakisK
2K Followers 519 Following Author and editor of books intended to help non-experts understand science. Latest book: "Ancestry Reimagined: Dismantling the Myth of Genetic Ethnicities"
PLOS Comp Biol @PLOSCompBiol
22K Followers 405 Following An open-access, peer-reviewed journal. Tweets from: PLOS CB Team. Header Image Credit: Benjamin Czaja, The University of Amsterdam.
Kim Pruitt @kdpru
408 Followers 453 Following Scientist manager of data resources. My roots are genetics, genomics, and annotation. Opinions expressed are my own.
Nitzan Gonen 💔 @gonen_nitzan
1K Followers 573 Following Group leader @Bar_ilan. Interested in sex determination, stem cells, and 3D genome organisation. Head of the BIU transgenic facility. ERC StG 2022. Mom of 4.
Eric Kernfeld @ekernf01
526 Followers 1K Following Statistician and computational biologist; uw alum; jhu student in @cahanlab, @alexisjbattle lab. He/him. https://t.co/jaMuFiHR9y
Johannes Bj{\"o}rk @AwfulDodger
2K Followers 3K Following Clinical metagenomics thru the lens of ecology and evolution with a healthy dose of statistics || @SeeraveF @WeersmaLab @groMicrobiome @stn_wame
Sheila Roitman @SheilaRoitman
895 Followers 971 Following Moving from Sci-Fi to Science 🔬📚🪴🤿🏕️🇦🇷 🇮🇱 Post-doc at WeigelWorld 🇩🇪, Plants & microbes Past: PhD at Beja Lab, Marine microbiology
Vera Beilinson @VeraBeilinson
91 Followers 181 Following Squid-vibrio symbiosis 🦑 | wet + dry lab 🧪 💻 | PhD Student in the McFall-Ngai Lab + Pachter Lab @Caltech l Computational and Applied Mathematics @UChicago
Steven Quartz PhD @StevenQuartz
1K Followers 469 Following Professor @Caltech. Neuroscience & neurophilosophy of reward, ethics, welfare. Computational neuroscience. Human origins. Cyclist pursuing masters hour record.
Nathan LaPierre @nlapier2
230 Followers 637 Following Computational biology, causal inference, and ML. Postdoc at @UChicago @HGEN_UChicago with @xinhe2 and @mstephens999. Prev PhD in CS @UCLA. Like ≠ endorse.
Varga Julia @jvarga92
424 Followers 2K Following PhD student at @HebrewU, working on SLIMs of the ubiqutin system. Member of @UbiMotif network and @FurmanLab
Ole Peters @ole_b_peters
28K Followers 383 Following Physicist, Ergodicity Economics @LdnMathLab. External Professor @sfiscience. Blog and mailing list: https://t.co/0K11DFH0W2
Comment motivated by single cell RNA seq, but applies throughout the sciences
An Icelandic drama in 3 acts
@lpachter Me today showing your tweet to my class during journal club where the paper discussed showed a "significant correlation" with R^2=0.06 and P=0.001.
Today the one and only @anamariaelek defended her thesis, the first PhD in our group. Many thanks to the commitee members @Chema_MD @larsplus and @MargaridaMCM
A funny thing happened on the way to routine single nucleus ATAC-seq analysis…and after scratching at it for longer than we wanted, we wrote a paper about what we found. This is a 🧵 about our little paper...(sorry long) biorxiv.org/content/10.110… 1/
Inspired by @lpachter and team's exploration of scRNA-seq pipelines, we face similar challenges in scATAC-seq, only magnified! After 5 years of tackling these inconsistencies with my advisor @JunhyongKim , Here is a summary (and some solutions😃) 1/n #Genomics #Bioinformatics
The choice of whether to use Seurat or Scanpy for single-cell RNA-seq analysis typically comes down to a preference of R vs. Python. But do they produce the same results? In biorxiv.org/content/10.110… w/ @Josephmrich et al. we take a close look. The results are 👀 1/🧵
I'm so happy for this. Katie is one of the scientists I admire the most, for her science, kindness, and leadership. I am incredibly fortunate to have her as a colleague, collaborator, and friend.
Katie Pollard has been named a lifetime @aaas Fellow for her pioneering work in computational biology, bioinformatics, and genomics. Read more about the award and Pollard's career on our website 👉 bit.ly/3UnwMgY
So, seqspec has been published. This is a good opportunity to remind everybody that your count matrix, R object, h5ad etc are NOT your raw data. Raw data are fastq files which are only useful when you know the content of your reads. Then ... 1/7 academic.oup.com/bioinformatics…
@MCATstudySesh @NatureMicrobiol Thank you, and you are absolutely right. We can now integrate decades of data on chemotaxis, and this comprehensive understanding opens up numerous exciting avenues. I have discussed some of these in a 'Behind the Paper' blog post here: go.nature.com/3xLFcWr
The most memorable moment of an AI seminar a couple years back was when the speaker, without irony, drew a yellow box labeled “black box”
Black box models are named after “black boxes”… which to be clear are recording devices built into airplanes solely for the purpose of explainability.
(1/3) Excited to share our newest publication!! Fun collaboration with the Chen and Severinov labs to investigate how the fluoride riboswitch rearranges a pseudoknot to form a terminator. See movie generated by @elisew00 and Alan Chen (@TheRNAInstitute) academic.oup.com/nar/article/do…
In order to further the development of an open database of scientific illustrations for the life sciences we have now set up a non-profit under the umbrella of @OC_Europe 1/ opencollective.com/bioicons
I love techbro hubris. They 'solved' protein folding literally by relying on millions of hours of PhD level experiments to train their model. The only way to understand the universe at the Plank scale is also by experiments, not by the hallucinations of some AI #coolaid
Deepmind's Demis Hassabis at TED tonight When asked about Microsoft + OpenAI spending $100B to train their next model: "Google will have spent more than that over time. To get to AGI, you need a lot of compute. Google still has the most compute." "With protein folding, we did…
Our paper "A machine readable specification for genomics assays" is now published in Bioinformatics, @OUPBioinfo. In short, we present a lightweight file format and command-line tool to document the structure of sequencing reads. Coauthored with @XiChenUoM and @lpachter. Paper:…
The @NCBI Sequence Read Archive has no documentation for the SRA file format which is used to host its massive 31 Pb dataset. github.com/ncbi/sra-tools…
Much more about the properties of eigenvalues and eigenvectors when a matrix is perturbed by noise in each entry.
What, if anything, do you wish you had know in grad school?
@lpachter When I worked with cancer registry data (i.e., hundreds of thousands of records), we'd get small p-values even if the slope of the regression line was close to 0; the statistician explained that was a artifact of having a very large sample size.
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