Accelerating and supporting the effective sharing and reproducibility of functional genomics data. Tweets by @trutane, @bffo

Joined February 2010
23 Photos and videos
FGED Society retweeted
Huge loss for the biomedical data science community ๐Ÿ˜ข 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. #RIP๐Ÿ™
14 Jun 2025
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 ๐Ÿ’”. Atul was a giant in so many ways. He was a visionary leader in translational bioinformatics @Stanford who reinvented himself as a pioneer of AI in medicine @UCSF. He published hundreds of papers, founded multiple companies, was elected to the National Academy of Medicine, and recently to the American Academy of Arts & Sciences. But Atul was much more than his achievements. He possessed something rare in science - infectious positivity. Every encounter with him, no matter how low I felt going in, I'd leave optimistic and energized to pursue my goals. After every talk he gave, students would line up to tell him how he motivated them to do something big with their lives. Another rare trait was his kindness and generosity with credit. Atul taught me: "credit is indefinitely divisible." In a field where people often take undeserved credit, this was inspiring. I will miss Atul, like so many others will. He is survived by his wife Gini and daughter Kimi, but his legacy will live on through his countless trainees and colleagues worldwide.
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FGED Society retweeted
24 Apr 2025
Government word search is killing my cutting-edge research statnews.com/2025/04/23/us-bโ€ฆ โ€” by @johnquackenbush โ€œโ€ฆfalling victim to a nationwide, indiscriminate destruction of university-based biomedical researchโ€ฆโ€ due to the use of โ€˜forbiddenโ€™ words. #NIHFundingCuts #DefendScience
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FGED Society retweeted
Benchmarking of variant calling software for whole-exome sequencing using gold standard datasets nature.com/articles/s41598-0โ€ฆ ๐Ÿงฌ๐Ÿ–ฅ๏ธ๐Ÿงช
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FGED Society retweeted
Are AI Tools Replacing Scientific Writing? Here's what some leading scientists have to say โคต Repost & Save (with ๐˜ค๐˜ญ๐˜ช๐˜ฑ๐˜ฑ๐˜ฆ.๐˜ฎ๐˜ฆ) โ€” Tools like ChatGPT are good helpers (but poor creators) โ€” AI can speed up writing (but it's not ready to take over scientific thinking). โ€” The real question isn't if we should use AI... ... but how to use it wisely! ๐Š๐ž๐ฒ ๐๐ž๐ง๐ž๐Ÿ๐ข๐ญ๐ฌ ๐จ๐Ÿ ๐€๐ˆ ๐ข๐ง ๐’๐œ๐ข๐ž๐ง๐ญ๐ข๐Ÿ๐ข๐œ ๐–๐ซ๐ข๐ญ๐ข๐ง๐  โคต ๐—ช๐—ฟ๐—ถ๐˜๐—ถ๐—ป๐—ด ๐—”๐˜€๐˜€๐—ถ๐˜€๐˜๐—ฎ๐—ป๐—ฐ๐—ฒ โ€” Helps break through writer's block โ€” Makes helpful suggestions for titles & abstracts โ€” Supports non-native English speakers with clear writing ๐—ฆ๐˜๐—ฟ๐˜‚๐—ฐ๐˜๐˜‚๐—ฟ๐—ฒ & ๐—ฅ๐—ฒ๐—ณ๐—ฒ๐—ฟ๐—ฒ๐—ป๐—ฐ๐—ฒ๐˜€ โ€” Breaks complex topics into manageable pieces โ€” Spots relevant papers you might have missed โ€” Helps organize thoughts & arguments ๐Œ๐š๐ฃ๐จ๐ซ ๐‚๐จ๐ง๐œ๐ž๐ซ๐ง๐ฌ โ€” AI can't do deep analysis or generate true insights โ€” Risk of shallow, cookie-cutter science writing โ€” Tools might generate false references or incorrect info โ€” Over-reliance could hurt students' learning Page 1/3
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10 Apr 2025
Researchers ๐Ÿงช 72% say there's a reproducibility crisis in biomedicine, 27% say it's significant ๐Ÿงช 62% say pressure to publish โžก๏ธ irreproducibility Institutions ๐Ÿฅผ 16% had procedures to enhance reproducibility ๐Ÿฅผ 67% value new research > replication studies #biomedicalResearch
Biomedical researchersโ€™ perspectives on the reproducibility of research journals.plos.org/plosbiologโ€ฆ ๐Ÿงฌ๐Ÿ–ฅ๏ธ
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10 Apr 2025
"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.โ€ฆ
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FGED Society retweeted
Among 143 replications of 56 experiments, less than half of biomedical research from Brazil was replicable, researchers found. biorxiv.org/content/10.1101/โ€ฆ
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FGED Society retweeted
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
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FGED Society retweeted
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/1igrbโ€ฆ

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FGED Society retweeted
At @cOAlitionS_OA we are envisioning a community-based scholarly communication system fit for #OpenScience in the 21st century, based on five principles. ๐ŸŸ coalition-s.org/towards-respโ€ฆ Follow this thread ๐Ÿงตfor a quick overview! #OpenAccess #ResponsiblePublishing [1/7]
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FGED Society retweeted
Ah, I've wanted this table on data sharing repositories for a while! Very nice. cell.com/action/showPdf?pii=โ€ฆ
20 Jan 2024
Some sharing solutions: cell.com/cell-genomics/fulltโ€ฆ
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FGED Society retweeted
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.
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FGED Society retweeted
Automated Bioinformatics Analysis via AutoBA ๐Ÿคจ biorxiv.org/content/10.1101/โ€ฆ Prompt it with experimental designs, it provides "plans" and code. github.com/JoshuaChou2018/Auโ€ฆ
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FGED Society retweeted
30 Oct 2023
GISAID in crisis: can the controversial COVID genome database survive? nature.com/articles/d41586-0โ€ฆ ($) @theosanderson had his @GISAID data access cut off w/out explanation, then restored after his story went โ€˜viralโ€™๐Ÿ‘‡ #SARSCoV2 #sequence #Pathogen #DataSharing

Replying to @theosanderson
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/d41586-0โ€ฆ
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FGED Society retweeted
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/S0092โ€ฆ Paper 2: scATAC GWAS Epigenome Erosion cell.com/cell/fulltext/S0092โ€ฆ Paper 3: Microglia States reprogramming cell.com/cell/fulltext/S0092โ€ฆ Paper 4: DNA damage gene fusions cell.com/cell/fulltext/S0092โ€ฆ MIT News: news.mit.edu/2023/decoding-cโ€ฆ Issue: cell.com/cell/current News & Views: cell.com/cell/fulltext/S0092โ€ฆ
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FGED Society retweeted
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/scidataโ€ฆ
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FGED Society retweeted
Are you an R user who is interested in learning Python ๐Ÿ ? 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 ๐Ÿ›ซ rebeccabarter.com/blog/2023-โ€ฆ #rstats #python #DataScience

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FGED Society retweeted
16 Jun 2023
Opinion piece: A better kind of #ReviewArticle? โ€œFlexible synthesisโ€ can deliver tailored and timely evidence for #research and #policy: ow.ly/fqYC50OQkju #MetaAnalysis #EvidenceBasedPolicy
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FGED Society retweeted
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

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FGED Society retweeted
11 Jul 2022
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/10.1101/โ€ฆ (note: analysis was based on data ca. 2013) #ISMB2022 #OpenScience
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