FGED Society @FGED
Accelerating and supporting the effective sharing and reproducibility of functional genomics data. Tweets by @trutane, @bffo FGED.org Worldwide Joined February 2010-
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Huge loss for the biomedical data science community 😢 Atul Butte @atulbutte left us yesterday at the way-too-young age of 55. Co-founder of @PersonalisInc (where I worked) + other biotechs, director of @UCSF_BCHSI, and a major #OpenScience advocate. He will be missed. #RIP🙏
Between alarms and sheltering, I learned last night that my postdoc mentor, Professor Atul Butte @atulbutte, has passed away, and he is only 55 years old. This is devastating news 💔. Atul was a giant in so many ways. He was a visionary leader in translational bioinformatics
Government word search is killing my cutting-edge research statnews.com/2025/04/23/us-… — by @johnquackenbush “…falling victim to a nationwide, indiscriminate destruction of university-based biomedical research…” due to the use of ‘forbidden’ words. #NIHFundingCuts #DefendScience
Benchmarking of variant calling software for whole-exome sequencing using gold standard datasets nature.com/articles/s4159… 🧬🖥️🧪
Are AI Tools Replacing Scientific Writing? Here's what some leading scientists have to say ⤵ Repost & Save (with 𝘤𝘭𝘪𝘱𝘱𝘦.𝘮𝘦) — Tools like ChatGPT are good helpers (but poor creators) — AI can speed up writing (but it's not ready to take over scientific thinking). — The real question isn't if we should use AI... ... but how to use it wisely! 𝐊𝐞𝐲 𝐁𝐞𝐧𝐞𝐟𝐢𝐭𝐬 𝐨𝐟 𝐀𝐈 𝐢𝐧 𝐒𝐜𝐢𝐞𝐧𝐭𝐢𝐟𝐢𝐜 𝐖𝐫𝐢𝐭𝐢𝐧𝐠 ⤵ 𝗪𝗿𝗶𝘁𝗶𝗻𝗴 𝗔𝘀𝘀𝗶𝘀𝘁𝗮𝗻𝗰𝗲 — Helps break through writer's block — Makes helpful suggestions for titles & abstracts — Supports non-native English speakers with clear writing 𝗦𝘁𝗿𝘂𝗰𝘁𝘂𝗿𝗲 & 𝗥𝗲𝗳𝗲𝗿𝗲𝗻𝗰𝗲𝘀 — Breaks complex topics into manageable pieces — Spots relevant papers you might have missed — Helps organize thoughts & arguments 𝐌𝐚𝐣𝐨𝐫 𝐂𝐨𝐧𝐜𝐞𝐫𝐧𝐬 — AI can't do deep analysis or generate true insights — Risk of shallow, cookie-cutter science writing — Tools might generate false references or incorrect info — Over-reliance could hurt students' learning Page 1/3
Researchers 🧪 72% say there's a reproducibility crisis in biomedicine, 27% say it's significant 🧪 62% say pressure to publish ➡️ irreproducibility Institutions 🥼 16% had procedures to enhance reproducibility 🥼 67% value new research > replication studies #biomedicalResearch
Biomedical researchers’ perspectives on the reproducibility of research journals.plos.org/plosbiology/ar… 🧬🖥️
"quality imbalance btwn groups of samples can significantly reduce relevance of differential genes, reducing reproducibility btwn studies. Appropriate expt'l design & analysis methods can substantially reduce the problem." #RNAseq #geneExpression #transcriptome #transcriptomics
Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets genomebiology.biomedcentral.com/articles/10.11…
Among 143 replications of 56 experiments, less than half of biomedical research from Brazil was replicable, researchers found. biorxiv.org/content/10.110…
I told a joke about data sharing, it's available upon request
I told a joke about scientific publishing but three people had to secretly weigh in before anyone could decide if it was funny
Excited to share our review paper in Cell! With @SashaGusevPosts @s_ramach @yang_i_li we discuss the genetic and molecular architecture of human traits, future opportunities and challenges and ways forward. authors.elsevier.com/a/1igrbL7PXqPfU
At @cOAlitionS_OA we are envisioning a community-based scholarly communication system fit for #OpenScience in the 21st century, based on five principles. 🟠coalition-s.org/towards-respon… Follow this thread 🧵for a quick overview! #OpenAccess #ResponsiblePublishing [1/7]
Ah, I've wanted this table on data sharing repositories for a while! Very nice. cell.com/action/showPdf…
@arjunrajlab @vsbuffalo Some sharing solutions: cell.com/cell-genomics/…
I think the sad actual answer to "What is the biggest open challenge in biology?" is: 1. Getting people to share data. 2. Structuring, organizing, and annotating data with metadata so it's useful. 3. Building higher-level abstractions so people can efficiently work with big data.
Automated Bioinformatics Analysis via AutoBA 🤨 biorxiv.org/content/10.110… Prompt it with experimental designs, it provides "plans" and code. github.com/JoshuaChou2018…
GISAID in crisis: can the controversial COVID genome database survive? nature.com/articles/d4158… ($) @theosanderson had his @GISAID data access cut off w/out explanation, then restored after his story went ‘viral’👇 #SARSCoV2 #sequence #Pathogen #DataSharing
It is bizarre that this key global infrastructure for pathogen sharing is subject to unpredictable gatekeeping with no clear policies. GISAID announced that it would set out reforms in the "coming weeks and months". That was in May: any news? [3/3] nature.com/articles/d4158…
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/… Paper 2: scATAC + GWAS + Epigenome Erosion cell.com/cell/fulltext/… Paper 3: Microglia States + reprogramming cell.com/cell/fulltext/… Paper 4: DNA damage + gene fusions cell.com/cell/fulltext/… MIT News: news.mit.edu/2023/decoding-… Issue: cell.com/cell/current News & Views: cell.com/cell/fulltext/…
I'm pleased to share a beta version of SciDataFlow, a command-line tool to track changes to data in research projects, push and pull data to remote repositories like Zenodo and FigShare, concurrently download tons of data, and more! github.com/vsbuffalo/scid…
Are you an R user who is interested in learning Python 🐍 ? My new blog post introducing Python from an R user's perspective might be just the launching point you need to get started on your journey 🛫 rebeccabarter.com/blog/2023-09-1… #rstats #python #DataScience
Opinion piece: A better kind of #ReviewArticle? “Flexible synthesis” can deliver tailored and timely evidence for #research and #policy: ow.ly/fqYC50OQkju #MetaAnalysis #EvidenceBasedPolicy
Interesting bit here on the requirements for data storage through FAIR principles and the economic and ecological costs of long-term storage of large quantities of data. #FAIR #OpenScience #datascience #structbio arxiv.org/abs/2301.01189
@GigaScience @serghei_mangul Nice work & important for improving #reproducibility & #FAIRdata in public omics data. Interesting to compare with transcriptome data compliance with the #MINSEQE minimum info standard: biorxiv.org/content/10.110… (note: analysis was based on data ca. 2013) #ISMB2022 #OpenScience
FAIRlady @SusannaASansone
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John M Hancock 🇬�... @JohnMHancock
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Billy 🌹 @nothingclever
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Alexandre Irrthum @AlexIrrthum
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Institute of Science ... @IseUsj
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Phoebe Magdy @MagdyPhoebe
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GenEmbryomics @genembryomics
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The Neuro @TheNeuro_MNI
12K Followers 3K Following Official account of #TheNeuro, Montreal Neurological Institute-Hospital. Follow for the latest on transforming research & care, improving lives via #OpenScience
MSI @shahidkooria
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drsona1 @drsona1
162 Followers 2K Following #PhD, #Bioinformatics, #Biology, #Immunology, #Computing
Tom Davy @TomDavy_
480 Followers 2K Following Functional Evolutionary Genomics PhD Student @TheCrick in @Pontus_Skoglund lab. Interested in hominins, proteins and classic Sci-Fi 🚀
Lionel Andrew Perkin @dandylionel
181 Followers 8K Following psychology, philosophy, holistic wellbeing, conscient, conciogenic informatics, agenic intelligence, sexual grace, salutogenics THEOPSYMANTIC Incohersive money
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175 Followers 602 Following
Liviu Vlăduțu @vliviu
112 Followers 870 Following Lecturer, Senior Researcher, Data Scientist, AI/ML Enthusiast, PhD, MSc
FAIRlady @SusannaASansone
3K Followers 880 Following Academic Lead #ResearchPractice @UniofOxford; Prof @oxengsci; Director @OxfordeResearch; #FAIRprinciples author; @FAIRsharing_org @isatools #FAIRcookbook colead
Jason "boundless deli... @JasonWilliamsNY
6K Followers 4K Following Asst. Dir. @DNALC @CSHL/ @CyVerseOrg /@thecarpentries/#AreciboC3/ #Foodie #ClassicalMusic #StarTrek /lifescitrainers.org —my own opinions.
@fairsharing.bsky.soc... @FAIRsharing_org
2K Followers 291 Following Registry of interrelated #repositories #standards #policies; in the process of transferring to Bluesky
Philippe Rocca-Serra @Phil_at_OeRC
400 Followers 448 Following
Steven Salzberg 💙�... @StevenSalzberg1
19K Followers 256 Following Bloomberg Distinguished Professor of BME, CS, and Biostats at Johns Hopkins Univ., tennis player, https://t.co/xwqVB2TYkL, @stevensalzberg.bsky.social
Chris Mason @mason_lab
12K Followers 974 Following Professor of Genomics, Physiology, & Biophysics @WeillCornell Medicine. Co-Founder / COI @BiotiaNYC, @UrsaBio & @Onegevity (@thornehealth)
Center for Open Scien... @OSFramework
33K Followers 1K Following We promote openness, integrity, and reproducibility in science. https://t.co/l3rtSA4VjT. Also tweet from @osfprereg, @RegReports, @OSKB_COS, and OSF help @OSFSupport.
FAIRplus @FAIRplus_eu
929 Followers 628 Following @IHIEurope project to improve data management and data governance in European health research. Coordinated by @ELIXIREurope and @JanssenGlobal
@allysonlister@fedisc... @allysonlister
806 Followers 589 Following @allysonlister.bsky.social Permanently moved from Twitter; please find me on Mastodon or Bluesky. Account retained for transparency.
David States MD PhD @statesdj
10K Followers 2K Following Chief Science/Medical Officer Angstrom Bio, Austin, TX COI: Our company is developing high throughput diagnostics @statesdj on other platforms
Lior Pachter @lpachter
68K Followers 2K Following Bren Professor of Computational Biology @caltech. Blog at https://t.co/FFQzhEsmhi. Tweets represent my views, not my employer's. #methodsmatter
Ewan Birney @ewanbirney
47K 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.
National Human Genome... @genome_gov
79K Followers 379 Following Funding research at the forefront of genomics to improve human health. Formerly the Human Genome Project. https://t.co/4hdQRFkFNU
Michael Hoffman @mich... @michaelhoffman
23K Followers 6K Following Chair, Comp Bio & Medicine Program, Princess Margaret Cancer Centre, @UHN. Assoc Prof, Medical Biophysics, University of Toronto. COI https://t.co/CvupKNIjZr
Razia Aliani @RaziaAliani
11K Followers 202 Following #3 most influential LinkedIn voice in AI for research | Epidemiologist | Systematic Reviewer | Biostatistician | 125K+ LinkedIn https://t.co/R18oaezmh5
Dr. Catharine Young @DrCatharineY
39K Followers 20K Following Scientist || Immigrant || Senior Fellow @HarvardChanSPH || Fmr: White House #CancerMoonshot, @CornellBME, @TEDFellow || 🇿🇦 + 🇺🇸
Geneskool @geneskool
121 Followers 444 Following Genome BC's Geneskool provides a variety of resources and programs for students in grades 9 through 12 that make learning about genomics fun.
cOAlition S @cOAlitionS_OA
6K Followers 310 Following Making full & immediate #OpenAccess to scientific publications a reality Also on: https://t.co/oYpmE3ee8E & https://t.co/hKUNcUINu3
Ming "Tommy" Tang @tangming2005
46K Followers 3K Following Director of bioinformatics at AstraZeneca. YouTube at chatomics. On my way to helping 1 million people learn bioinformatics. Also talks about leadership.
Nicky Mulder @Nicky_Mulder
4K Followers 40 Following @H3ABioNet PI and Head of UCT Computational Biology Division. Passionate about Genomics and developing Bioinformatics capacity in Africa.
H3ABioNet @H3ABioNet
9K Followers 314 Following H3ABioNet is a Pan African Bioinformatics network supporting @H3Africa researchers & projects,developing Bioinformatics capacity within Africa. RTs≠ endorsement
GISAID Initiative @GISAID
12K Followers 29 Following 15 Years of Real-Time Communication in Disease Prevention
PNASNews @PNASNews
183K Followers 1K Following Cutting-edge news & reports from PNAS, one of the world's most-cited scientific journals, sibling journal of @PNASNexus & an official journal of @theNASciences.
Serghei Mangul #Ukrai... @serghei_mangul
2K Followers 2K Following Assistant Prof. #NewPI @USCMann. We develop and apply bioinformatics methods to large-scale omics data. Husband and father of 2+1 Слава Україні
Prof Zornitza Stark @ZornitzaS
2K Followers 1K Following Clinical Geneticist, @TeamVCGS @AusGenomics @PanelAppAus @RCHMelbourne @MCRI_for_kids #AcuteCareGenomics. Professor @UniMelbMDHS. All views are my own.
Helen Bevan @HelenBevan
137K Followers 21K Following Change facilitator, strategist, speaker. Prof. of Practice in Health & Care Improvement @WarwickBSchool. Advisor @HorizonsNHS. Senior Fellow @TheIHI. Views own.
Bioinfocodes @bioinfocodes
1K Followers 18 Following @bioinforange ENG #bioinformatics #computationalbiology #biology Contact: [email protected] Founder: @mcaliseki1
scverse @scverse_team
4K Followers 0 Following Foundational tools for omics data (mostly in python) Join us at Bluesky: https://t.co/ziA75N5PZp
@OntoCommons @ontocommons
713 Followers 537 Following #OntoCommons is an @EU_H2020 project delivering a #FAIR #interoperable #standardised #ontology #datadocumentation for faster & trustworthy #datasharing
OpenSci Talk @OpenSciTalk
4K Followers 1 Following Community broadcaster bot, multilingual sibling of @OpenSci_News Use #OpenScience or #OpenSciTalk for RTs. (Human: @dipanshunagar)
TU Wien Research Data... @RDMTUWien
470 Followers 319 Following We support researchers @tu_wien handling research data and code throughout the entire life cycle. #researchdata #RDMsupport #DMP #FAIRdata #OpenScience
The International Bun... @intbunch
171 Followers 139 Following What good is an idea if it can't be shared? We were founded to foster collaboration and share ideas. The more you share your ideas, the more impact they have.
Pôle National de Don... @PNDBiodiv
376 Followers 496 Following Pôle de {méta}données de biodiversité @dataterra & centre de référence thématique @recherchedatagv | French Hub in Biodiversity Research Data & Ecoinformatics
FAIR Data Podcast @FAIRdataPodcast
398 Followers 197 Following All things FAIR - Findable, Accessible, Interoperable and Reusable. Join Rory Macneil and new guests every Wednesday on Spotify, Apple and Google Podcasts!
Klaus Tochtermann @ktochtermann
951 Followers 100 Following Director ZBW - Leibniz-Information Centre for Economics, Professor for Computer Science, #OpenScience #Cloud #ResearchData #DigitalScience #EOSC #NFDI
International Common ... @ICDAbio
1K Followers 76 Following ICDA aims to improve prevention, diagnosis, and treatment of common diseases by accelerating discovery from genetic maps to biological mechanisms to medicine
Lappalainen Lab @tuuliel_lab
5K Followers 578 Following Functional human genomics @ KTH, SciLifeLab, NY Genome Center. Pro science here, more fun stuff fun at @tuuliel. Mastodon [email protected]
NU Biotech Group @Biotech_at_NU
91 Followers 103 Following Biotech Group @: NU Student Organization We provide the tools and connections for Northwestern graduate students to excel in the Biotech industry.
Martin Larralde @althonos
479 Followers 676 Following From Paris, PhD candidate in Bioinformatics, @ZellerGroup at @EMBL, associated @crc1371 PhD student. Open-source enthusiast and wannabe poet.
Pao Corrales @PaobCorrales
934 Followers 372 Following Lic. en Cs. de la Atmósfera, miembro de @Exp_Ciencia, @thecarpentries y @RLadiesGlobal entre otras comunidades :)
cineca-project @CinecaProject
519 Followers 104 Following @EU_H2020 consortium to facilitate transcontinental cloud-based human data exchange to accelerate disease research and improve health.
Imran S. Haque (@ihaq... @ImranSHaque
2K Followers 850 Following CTO at @Kimia_Tx. Fmr SVP AI @RecursionPharma; ex-Stanford(PhD), forever Cal 🐻. Find me at https://t.co/LPj0As74Em if the alternative handles get banned.
dana_peer @dana_peer
15K Followers 166 Following
Mo Lotfollahi @mo_lotfollahi
13K Followers 4K Following ML for biology and drug discovery | Faculty @sangerinstitute @Cambridge_uni
ArrayExpress @ArrayExpressEBI
451 Followers 129 Following Functional Genomics Submissions @emblebi All data freely available in the ArrayExpress Collection @BioStudiesEBI #bioinformatics #genomics #opendata #FAIR
Stephen Piccolo @stevepiccolo
653 Followers 274 Following Associate Professor of Biology at Brigham Young University in Provo, UT (USA). Bioinformatics, genomics, data science, informatics education (opinions my own).
Arvind @DrArvindMer
130 Followers 254 Following Postdoc fellow at @pmcancercentre Research: Bioinformatics & Precision Medicine in Cancer
HHS @HHSGov
1.7M Followers 40 Following Official account of the U.S. Department of Health & Human Services | Follow @SecKennedy | For latest news follow @HHSResponse | MAHA 🇺🇸
eLife - the journal @eLife
176K Followers 698 Following The funder-researcher collaboration and open-access journal for research in the life and biomedical sciences | @eLifeCommunity
STAR Protocols @STARProtocols
5K Followers 211 Following STAR Protocols offers open access peer-reviewed protocols that are structured, transparent, accessible & reproducible. Lead Editor Jeremy Petravicz @JeremyNeuro
Mol Syst Biol @MolSystBiol
7K Followers 845 Following #OpenAccess @EMBOpress journal publishing pioneering research in systems & synthetic biology, systems medicine Bluesky: @molsystbiol.bsky.social
Holly Witteman, PhD �... @hwitteman
12K Followers 4K Following Professor, Canada Research Chair in Human-Centred Digital Health @wittemanlab PhD human factors engineering #T1D since 83 #insulin4all #DisabledInSTEM mom En/Fr
Reproducibility for E... @repro4everyone
960 Followers 540 Following Reproducibility for Everyone! Enabling researchers worldwide to adopt best practices in #reproducibility and teach others through workshops. Join us! #R4E
CODATA @CODATANews
6K Followers 2K Following CODATA is the Committee on Data of the @ISC. We support the advancement of science as a global public good by promoting Open Science and FAIR data.
EOSC Secretariat @EoscSecretariat
2K Followers 606 Following We supported the #EOSC Governance to co-create the European Open Science Cloud. Project closed in October 2021, please follow @EoscAssociation for updated info.
EOSC-hub @EOSC_eu
3K Followers 342 Following Integrating and managing services for the European Open Science Cloud #EOSChub #EOSC #OpenScience #H2020 #openaccess
Natalie Harrower @natalieharrower
3K Followers 2K Following Executive Director of CRDCN: https://t.co/w9E4bOSmYW #ResearchData #FAIR #HSS #ResearchInfrastructures (She/her). Try me at @natalieharrower.bsky.social
Retraction Watch @RetractionWatch
93K Followers 19 Following Daily newsletter https://t.co/T4dNEAd2zy Database https://t.co/Wx3LmYCtGk Tips [email protected] (better than @ replies) Donate https://t.co/qh4sIBw1uU
EpiExplorer @hEpiExplorer
49 Followers 81 Following EpiExplorer is a novel approach for interactive exploration of the largest public genetic and epigenetic datasets
Tony Burdett @TonyBurdett
60 Followers 155 Following Team Leader of the Archival Infrastructure and Technology at EMBL-EBIYou might like
