Yuchen Ge @YuchenGe1
PhD Candidate, Department of Biomedical Engineering @JHUBME, Johns Hopkins School of Medicine @HopkinsMedicine Baltimore, US Joined August 2014-
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Apparently @Nature has a serious concern that we were correct–that the cancer microbiome is just not there, as we described in our paper now published in @mbiojournal. The Nature paper now has an Editor's Note:
Apparently @Nature has a serious concern that we were correct–that the cancer microbiome is just not there, as we described in our paper now published in @mbiojournal. The Nature paper now has an Editor's Note: https://t.co/33baU8zeMh
.@StevenSalzberg1 kicking off the opening session of Genome Informatics on Major data analysis errors invalidate cancer microbiome findings. #gi2023 @CSHL
Our paper on the human gene annotation catalog CHESS, which now includes all of MANE and a more rigorous definition of genes of all types. With @elapertea @av_sparrow @thesteinegger @markusjsommer @ErdogduBeril @IliaMinkin and others: genomebiology.biomedcentral.com/articles/10.11…
Our paper debunking the 2020 cancer microbiome results is now published, in @mbiojournal. We'll see if @Nature (or the authors) will retract these deeply flawed results. h/t @ProfBootyPhD @EricTopol journals.asm.org/doi/10.1128/mb…
Our paper examining critical errors in a cancer metagenomics study is now live in @mbiojournal. Work carried out with @StevenSalzberg1 @danbrewer @elapertea @YuchenGe1 @JenniferLu717 and others. Errors in bioinformatics can be subtle but important! doi.org/10.1128/mbio.0…
Many of you would have seen that since releasing this and sending the pre-print to prospective journals, we have been collaborating with @StevenSalzberg1 @elapertea @YuchenGe1 @JenniferLu717 and others to take this analysis one step further. doi.org/10.1101/2023.0… 5/7
I think we need to talk about how devastating this cancer microbiome refutation paper from @StevenSalzberg1 and colleagues is. It really speaks to how devoid of critical thinking and intellectual depth our glam publishing ecosystem has become. 1/n biorxiv.org/content/10.110…
@anshulkundaje @tkorem @StevenSalzberg1 @phylogenomics For those interested I forked the rebuttal to the rebuttal and added the lines of code that look at feature importance. Its here github.com/travisgibson/t… and shout out to @multi_omics (Greg Sepich-Poore) for making the rebuttal^2 open source cc @gilbertjacka
@EricTopol @StevenSalzberg1 @AbrahamGihawi @YuchenGe1 @NewsfromScience has our story up on this dispute science.org/content/articl…
One of the most informative, eye-opening, well-written papers I've read in a while. I learned a ton! @AbrahamGihawi @YuchenGe1 @StevenSalzberg1 & others biorxiv.org/content/10.110…
A re-analysis of multiple studies that asserted the role of bacteria in cancer raises questions at to the veracity of the findings and the link biorxiv.org/content/10.110… @StevenSalzberg1 @AbrahamGihawi @YuchenGe1 and colleagues
We've learned a lot from the ChatGPT research preview and have been making important updates based on user feedback. ChatGPT will be coming to our API and Microsoft's Azure OpenAI Service soon. Sign up for updates here: share.hsforms.com/1u4goaXwDRKC9-…
I’M WONDERING WHEN WE WILL STOP SEEING OURSELVES AS HAVING JUST ONE COMPLETE GENOME, BUT INSTEAD HAVING A COLLECTION OF GENOMES WHERE EVERYONE’S DIFFERENCES ARE REPRESENTED.
Congratulations Dr. @alaina_shumate on successfully defending your Ph.D. thesis today! Outstanding work on Liftoff, StringTie, and other novel computational methods. H/T to committee members @elapertea @timp0
Only 26 days from submission to publication! The genome of the American groundhog, Marmota monax Daniela Puiu et al., published by @F1000Research f1000research.com/articles/9-113…
Esther Schroot @SchrooEsth
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Thomasena Pavloski @ThomasenaP21074
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Yin-Hong Cao @caoyinhong
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Annabelle 🤪 @Annabelle__C95
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Felipe F. Castro @drfelipefc
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219 Followers 4K Following Tasha specializes in adult products (silicone dolls) and provides you with the best quality service, please visit the Telegram channel for details.
Mateteigh @mateteigh76671
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Li Song @mourisl
1K Followers 3K Following 毛利元光. Assistant Prof. @BioMedDataSci. PostDoc @XShirleyLiu @lh3lh3 @dfcidatascience. PhD @JHUCompSci. Research on bioinformatics, algorithms. https://t.co/zRfJOaf6gD
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Marie @irvin_marie61
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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 ⬇️
Jen Lu @JenniferLu717
237 Followers 39 Following Staff Scientist in Microbial Genomics Bioinformatics, Author of Bracken and Kraken (2).
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Jhonata de Oliveira @JhonataGomesde3
31 Followers 691 Following Biomedical sciencist🔬. Clinical and laboratory analyst. Brazilian 🇧🇷. Science Promoter.
DC Maryland Virginia .. @DCBionetwork
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alex rubinsteyn @iskander
5K Followers 4K Following Genomics + immunology + ML = personalized cancer immunotherapy. @CompMedUNC @UNC_Lineberger @OpenVax https://t.co/8DWibdgbLI
Steven Salzberg 💙�.. @StevenSalzberg1
19K Followers 235 Following Bloomberg Distinguished Professor of BME, CS, and Biostats at Johns Hopkins University, tennis player, blogger at Forbes: https://t.co/7SZhlbYPtn…
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575 Followers 4K Following just a student in field of Genomics and Bioinformatics. let's talk science !! ☺☺
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Conan Zhao @ConanYZhao
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Jonathan Eisen @phylogenomics
66K Followers 10K Following Bio. Prof. @UCDavis "All microb(iom)es, all the time" Lab: https://t.co/XVzbMvveOE Ted talk: https://t.co/74jjCOFY90 Pics: https://t.co/waXqjRp6Pc
Larry J. Dishaw @LJDishaw
748 Followers 2K Following Dishaw Lab is interested in how secreted immune effectors shape the gut microbiome. Bacteria-phages-fungi. Integrative biology lab.
Stuart MacGowan @stuartmac44
440 Followers 1K Following Computational biologist | Protein structures & human variation | R & Python | Genetic effects on protein function | See: https://t.co/wzvNj7zDKI
Travis E Gibson @TravisEGibson
824 Followers 765 Following Assistant Professor @harvardmed, PI @bwhpath | @GibsonLab - ML and control for biology
Beril Erdogdu @ErdogduBeril
62 Followers 116 Following Ph.D. candidate at Johns Hopkins University researching in fields of computational biology, genomics, and transcriptomics.
Abraham @AbrahamGihawi
282 Followers 729 Following UEA Postdoc - Bioinformatics - Cancer (meta)genomics since 2017. Opinions are mine alone.
NeutronField @neutronfield
389 Followers 1K Following Showcase your AI text to image prompts and make money selling them.
Md Nobe Hosen Rana @romi_studio3
480 Followers 2K Following I am a Graphic Designer and Professional Photo Manipulation Designer with 10 years of experience working with clients and agencies from around the world.
The Isoform Explorer @IsoformExplorer
50 Followers 67 Following I'm on a mission to explore the human proteome, one isoform at a time
Kuan-Hao Chao @KuanHaoChao
249 Followers 217 Following CS PhD candidate in @StevenSalzberg1 & @ElaPertea lab at @JohnsHopkins @JHUCompSci 🧬💻 #NTUEE
Ed @edwardlww
61 Followers 848 Following
Ilia Minkin @IliaMinkin
614 Followers 750 Following A researcher in bioinformatics algorithms, postdoc at Steven Salzberg's lab. Views and opinions are mine only.
Li Song @mourisl
1K Followers 3K Following 毛利元光. Assistant Prof. @BioMedDataSci. PostDoc @XShirleyLiu @lh3lh3 @dfcidatascience. PhD @JHUCompSci. Research on bioinformatics, algorithms. https://t.co/zRfJOaf6gD
mBio @mbiojournal
28K Followers 369 Following The American Society for Microbiology’s first broad-scope, online-only, open-access journal. Contact us at [email protected].
RECOMB Conference Ser.. @RECOMBconf
1K Followers 248 Following The 28th International Conference on Research in Computational Molecular Biology. April 29 - May 2, 2024
Professor Booty PhD @ProfBootyPhD
5K Followers 5K Following Come for the science (genetics & cell biology), stay for the social justice, parenting, comedy and random crap. #BlackLivesMatter #heynongman #GARABA
Conan Zhao @ConanYZhao
392 Followers 1K Following MS2 @MayoClinicSOM (☢️🦀) PhD @QBioS_GT | @Gatechmicrobes | @sambrownlab (microbiomics ⋂ CF) JM @reininsarcoma Scholar 🇨🇦 posts are my own
Wes Wilson @WesleyWilson
9K Followers 5K Following Tumour Immunologist & Pulmonary Oncology @PennMedicine , Bioinformation, Perpetual Hockey Player, #SciComm #cancer Editor @SciSeeker, Host @TumorTalk
Eric Kernfeld @ekernf01
547 Followers 1K Following Statistician and computational biologist; uw alum; jhu student in @cahanlab, @alexisjbattle lab. He/him. https://t.co/jaMuFiHR9y
DC Maryland Virginia .. @DCBionetwork
954 Followers 5K Following Life science news and jobs from Washington DC, Maryland and Virginia. Part of @BiotechNetworks, connecting #biotech since 2008.
Johns Hopkins BME @JHUBME
5K Followers 180 Following The Johns Hopkins Department of Biomedical Engineering seeks to improve health through excellence in research, education, and technology.
Anshul Kundaje (anshu.. @anshulkundaje
22K Followers 2K Following Genomics, Machine Learning, Statistics, Big Data and Football (Soccer, GGMU). Post: @anshulkundaje, Threads: anshulkundaje
STAT @statnews
165K Followers 5K Following Reporting from the frontiers of health & medicine. Sign up for any of our 10 free newsletters here: https://t.co/CBx3GZBv31
Retraction Watch @RetractionWatch
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alex rubinsteyn @iskander
5K Followers 4K Following Genomics + immunology + ML = personalized cancer immunotherapy. @CompMedUNC @UNC_Lineberger @OpenVax https://t.co/8DWibdgbLI
John Travis @johnstravis
2K Followers 319 Following Managing News Editor for @NewsfromScience, former biology reporter @Science and @ScienceNews, Dee-troit loyal
Larry J. Dishaw @LJDishaw
748 Followers 2K Following Dishaw Lab is interested in how secreted immune effectors shape the gut microbiome. Bacteria-phages-fungi. Integrative biology lab.
Stuart MacGowan @stuartmac44
440 Followers 1K Following Computational biologist | Protein structures & human variation | R & Python | Genetic effects on protein function | See: https://t.co/wzvNj7zDKI
Travis E Gibson @TravisEGibson
824 Followers 765 Following Assistant Professor @harvardmed, PI @bwhpath | @GibsonLab - ML and control for biology
Jonathan Eisen @phylogenomics
66K Followers 10K Following Bio. Prof. @UCDavis "All microb(iom)es, all the time" Lab: https://t.co/XVzbMvveOE Ted talk: https://t.co/74jjCOFY90 Pics: https://t.co/waXqjRp6Pc
Beril Erdogdu @ErdogduBeril
62 Followers 116 Following Ph.D. candidate at Johns Hopkins University researching in fields of computational biology, genomics, and transcriptomics.
Abraham @AbrahamGihawi
282 Followers 729 Following UEA Postdoc - Bioinformatics - Cancer (meta)genomics since 2017. Opinions are mine alone.
Eric Topol @EricTopol
694K Followers 590 Following physician-scientist, author, editor. Ground Truths: https://t.co/YhatcBT0hA
Heng Li @lh3lh3
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Science Magazine @ScienceMagazine
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nature @Nature
2.6M Followers 4K Following Research, News, and Commentary from Nature, the international journal of science. For daily science news, get Nature Briefing: https://t.co/wGmQlQ8a4D
Science News @ScienceNews
5.1M Followers 555 Following Covering the latest news in all fields of science. Publisher @society4science. See also @SN_Explores.
Teachers & Researcher.. @TRUhopkins
3K Followers 497 Following Grad worker union at Johns Hopkins University | RT/follows≠endorsements. #JHUGradsRising #TRUisYOU. For bargaining updates: https://t.co/iSSyJB9jil…
𝕐 (@[email protected].. @nomad421
8K Followers 941 Following Associate Professor of CS @ University of Maryland. Proud Rust advocate! I ♥ science & compiled, statically-typed programming languages! Views are my own.
OpenAI @OpenAI
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The Isoform Explorer @IsoformExplorer
50 Followers 67 Following I'm on a mission to explore the human proteome, one isoform at a time
Kuan-Hao Chao @KuanHaoChao
249 Followers 217 Following CS PhD candidate in @StevenSalzberg1 & @ElaPertea lab at @JohnsHopkins @JHUCompSci 🧬💻 #NTUEE
Mathieu Alain @miniapeur
19K Followers 2K Following Researching @ai_ucl. Co-organises @uclcsml and @logconference. FR, EN, trying ES. 🇹🇼🇨🇦🇬🇳🇺🇸🇩🇴🇫🇷🇪🇸🇬🇧🇿🇦
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614 Followers 750 Following A researcher in bioinformatics algorithms, postdoc at Steven Salzberg's lab. Views and opinions are mine only.
Dr. Jean Fan @JEFworks
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Nature Biotechnology @NatureBiotech
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Feilim Mac Gabhann @FMacG
562 Followers 681 Following PI of @MacGLab at @ICM_JHU and @JHUBME. Co-EiC of @PLOSCompBiol. Alum of @UCD_ChemEng, @JohnsHopkins, & @UVABME. Fan of @DOE_SC_NSB.
Cold Spring Harbor La.. @CSHL
38K Followers 1K Following Non-profit research and educational institution at the forefront of molecular biology, cancer, neuroscience, plant biology, and genetics.
Paris Saint-Germain @PSG_inside
15.1M Followers 162 Following 🇺🇸🇬🇧@PSG_English🇪🇸🇺🇾🇨🇷@PSG_Espanol🇧🇷🇵🇹@PSGBrasil🇶🇦@PSG_Arab🇮🇩@PSGIndonesia🇯🇵@PSGJapan🇰🇷@PSG_KR👱♀️@PSG_Feminines🥋@PSG_Judo🤾♂️@PSGHandBIG surprise from #RECOMB2024 ! What an honor to receive the best paper award! Thanks @RECOMBconf for this wonderful conference with so many interesting talks and posters, and @BenLangmead for many insightful discussions! (Full paper link :D genomebiology.biomedcentral.com/articles/10.11…)
📢📢Dear friends, I'm thrilled to introduce LiftOn, our new homology-based annotation lift-over tool🚀 Join my talk at @RECOMBseq Saturday April 27th at 2:50PM! @JakobHeinz9 @celinehohzm @alan_mayonnaise @alaina_shumate @elapertea @StevenSalzberg1 🔗github.com/Kuanhao-Chao/L… (1/5)
check out the new paper from my PhD student Hayden (Hyun Joo) Ji, in which she uses #AlphaFold, splice site predictors, and other tools to identify hundreds of novel isoforms of human genes. Well done Hayden! biorxiv.org/content/10.110…
Apparently @Nature has a serious concern that we were correct–that the cancer microbiome is just not there, as we described in our paper now published in @mbiojournal. The Nature paper now has an Editor's Note:
Major, fatal errors found in the data and methods of a 2020 paper in @Nature, including millions of reads mis-identified as bacteria. The "cancer microbiome" in this study was simply not there. @AbrahamGihawi @elapertea @YuchenGe1 @JenniferLu717 biorxiv.org/content/10.110…
Excited to share our collaborative research on the Wheeler Graph Toolkit from Johns Hopkins and @Berkeley_EECS. Check out our new Wheeler graph recognition algorithm and findings in the @JHUCompSci post. Great collaboration with @PeiWeiChen, @BenLangmead, and Sanjit Seshia.
The human genome is biased—but rearranging it can help. Researchers including @BenLangmead and @KuanHaoChao release a new algorithm that promises to help restructure the human reference genome into a more powerful—and inclusive—graph-based representation. cs.jhu.edu/news/the-human…
Achievement unlocked: GitHub streak for a whole year!
good to be back in person at Genome Informatics–the first post-COVID meeting on site at CSHL since 2019. Looking forward to today's talks and keynote by Sean Eddy, and tomorrow's keynote by @khmiga #GI2023
.@StevenSalzberg1 kicking off the opening session of Genome Informatics on Major data analysis errors invalidate cancer microbiome findings. #gi2023 @CSHL
Thrilled to share the first preprint from my lab! We losslessly compressed FM-index using a novel technique called run-block compressed BWT (RBBWT). Building upon it, we implemented the Centrifuger method for taxonomic classification on sequencing data. biorxiv.org/content/10.110…
our new paper led by @IliaMinkin describes how we used a very large multi-genome alignment to discover a striking degree of conservation among most splice sites in protein-coding genes. The paper is now out in @biorxivpreprint
Our study with @StevenSalzberg1 of conservation of human splice sites across 470 mammalian genomes is out on bioRxiv: biorxiv.org/content/10.110… We assessed conservation consistency of "canonical dinucleotides" GT/AG flanking introns in different genome annotations and found:
.@StevenSalzberg1 kicking off the opening session of Genome Informatics on Major data analysis errors invalidate cancer microbiome findings. #gi2023 @CSHL
Our study with @StevenSalzberg1 of conservation of human splice sites across 470 mammalian genomes is out on bioRxiv: biorxiv.org/content/10.110… We assessed conservation consistency of "canonical dinucleotides" GT/AG flanking introns in different genome annotations and found:
Our paper on the human gene annotation catalog CHESS, which now includes all of MANE and a more rigorous definition of genes of all types. With @elapertea @av_sparrow @thesteinegger @markusjsommer @ErdogduBeril @IliaMinkin and others: genomebiology.biomedcentral.com/articles/10.11…
I should add that the authors of the 2020 paper commented to @science, when asked about our preprint, that they'd respond after our paper appeared in a peer-reviewed journal. Well, now that's happened
Our paper debunking the 2020 cancer microbiome results is now published, in @mbiojournal. We'll see if @Nature (or the authors) will retract these deeply flawed results. h/t @ProfBootyPhD @EricTopol journals.asm.org/doi/10.1128/mb…
Our paper examining critical errors in a cancer metagenomics study is now live in @mbiojournal. Work carried out with @StevenSalzberg1 @danbrewer @elapertea @YuchenGe1 @JenniferLu717 and others. Errors in bioinformatics can be subtle but important! doi.org/10.1128/mbio.0…
Our paper is out in @Nature! This is from a @cshlbanbury meeting where a group of scientists got together to ask, can we ever identify the complete set of human genes? And how do we do that? with @elapertea @av_sparrow @carninci and many others nature.com/articles/s4158…
We managed to build a splice site predictor that beats SpliceAI, the current state-of-the-art. SPLAM uses a convolutional neural net but w/a different design. Preprint and code are out; paper is under review. Great work by @KuanHaoChao biorxiv.org/content/10.110…
Keynote Speakers for #RECOMB2024 announced: James J. Collins, Shafi Goldwasser, Xihong Lin, Steven Salzberg and Phillip A. Sharp. We are so excited to hear these talks!
I missed this before, but this analysis by @Dereklowe in @science is definitely worth a read. He calls our paper (debunking the 2020 cancer microbiome @Nature paper) a "cruise missile" 🤣: science.org/content/blog-p…
A very intriguing result in the new Y chromosome paper, one that you might miss unless you read the paper closely... 1/6 nature.com/articles/s4158…
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