Samuel Ruiz @samuelruizperez
Joined February 2014-
Tweets125
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Followers19
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Following1K
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In a great collaboration with @HummerLab and the Kräusslich lab, @jpkreysing, @MaziarHeidari1, @VojtechZila and others tackle what happens when HIV capsid goes through an NPC. Instead of the NPC cracking the capsid, the capsid appears to crack the NPC (@MPIbp @CiidHeidelberg).
Totally wild story by @deMendoza_Alex: DNA methyl transferase unique to Amoebidium unicellular holozoan (sponge-like) silences various endogenous giant viruses and transposons! #icte2024 biorxiv.org/content/10.110…
Are you still struggling with the manual curation of TEs? Do you want to know the magic of cleaning TE MSAs with only a single button click? Welcome to try TEtrimmer (paper will come soon) github.com/qjiangzhao/TEt… I am also looking forward to discussing this with you in #ICTE2024
Do the mutations that drive evolution improve many traits or few? How might this change over the course of evolution? Excited to share our new work exploring these questions in the first 2 steps of adaptation w/ @liyuping927 @gsherloc @PetrovADmitri 🧵1/n biorxiv.org/content/10.110…
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
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:…
Publication alert ! Paper from helmholtz-munich.de/en/ife in @Nature How complex epigenetic modification signatures regulate genome function. With interactive online resource marcs.helmholtz-munich.de Big data ! @epigeneticsHMGU @HelmholtzMunich nature.com/articles/s4158…
Yeahhh uh can I get uhhh
Not all exons are protein coding: Addressing a common misconception Freely available top-read @CellGenomics paper @nickywhiffin @bdi_oxford @RNA_julie @ScienceLeeds @SBSatEd hubs.li/Q024LnnK0
Added gratuitous explosions and particle effects to the code editor I'm building
The Webb telescope has detected carbon dioxide and methane in the atmosphere of exoplanet K2-18 b, a potentially habitable world over 8 times bigger than Earth. Webb’s data suggests the planet might be covered in ocean, with a hydrogen-rich atmosphere: go.nasa.gov/3sGKNLe
A copy-paste model for chromatin states propagation suggests PTMs on old histones as blueprints for modifying ✏️ new histones. Is it true? 🤔 Do old histones carry epigenetic memory 🧠 crucial for keeping 🛠️ embryonic stem cell identity 🐭🧫? MCM2-2A, new tool to investigate. 2/n
🎉 Pipeline release! nf-core/atacseq 2.1.2- Iron Bull (ATAC-seq, peak-calling, and QC analysis pipeline) See the release notes: github.com/nf-core/atacse…
RNA covalently links to proteins: today in @Nature! #RNAylation as new post-translational modification (or #Proteinylation as new post-transcriptional RNA modification!) by @HoeferLab, @JaeschkeLab, @MaikSchauerte. Important during #phage infection! nature.com/articles/s4158…
Long reads are one of the greatest innovations for RNA profiling as they help to identify individual isoforms. But… what about long reads that don't perfectly match reference annotations? Very happy to share our answer to this question - bambu! nature.com/articles/s4159… 1/n
Excited to share SCARlink, a gene-level regression model for multiomic scRNA+scATAC-seq. SCARlink identifies regulatory regions in a cell-type-specific manner without relying on a peak-set and predicts gene expression from scATAC-seq that can drive chromatin potential analysis.
Excited to share SCARlink, a gene-level regression model for multiomic scRNA+scATAC-seq. SCARlink identifies regulatory regions in a cell-type-specific manner without relying on a peak-set and predicts gene expression from scATAC-seq that can drive chromatin potential analysis.
Making more progress on the T4 phage illustration. All the mRNA (viral and cellular) is in, added most of the cell wall, and just finished adding a bunch of chaperonins. Now I need to add lots and lots and lots of soluble molecules.
Transposable elements as essential elements in the control of gene expression dlvr.it/StsXPN
I could totally hang with Maul. redd.it/138fd5j
Robert A. Petit III, .. @rpetit3
2K Followers 2K Following Public health bacterial genomics, bioinformatic workflow development, and training. Bactopia (https://t.co/diBn3GGbqW). @ Wyoming Public Health Laboratory
Poppy Aeron Gould @DrPoppyGould
265 Followers 374 Following Postdoc in @LabRowe at @blizard_inst working on transposons, stem cells and development. She/her. 🏳️🌈
Mae Woods @maelouisewoods
746 Followers 704 Following Postdoc interested in compbio, HPC & math. Currently working in immunology & immunotherapy GitHub https://t.co/ql99gQpTJ4 always happy to share code/ideas
Kirk Lohmueller @lohmueller
4K Followers 3K Following Population geneticist and Professor at UCLA. Traffic Ninja. Dad. He/him.
Jacob Valdez @jvboid
2K Followers 8K Following surfing a 2nd order phase transition | building @HumanRobotsAI | [email protected] | +1.469.968.9490 | https://t.co/V5Odmcls1F
AxonDAO @AxonDAO
16K Followers 5K Following Building the future of #DeSci 🌐 NVIDIA AI Inception | Official $AXGT token updates 👉 https://t.co/dHsKVUcmNH
APOideas @APOideas
397 Followers 827 Following A strange loop. "I am the heavy mountain, this is the gentle thunder — roll on down".
Karla TA @karla_ta3
14 Followers 39 Following PCB, UNAM This is me trying (on social media) Graduate student by day, wanderlust enthusiast by night
Anja Groth 🇺🇦 @groth_anja
2K Followers 831 Following Professor at UCPH #NNFCPR Interests are epigenetics, genome maintenance, aging & cancer, creativity & innovation, society in general. Opinions are my own.
Rachel Luu @rachelkluu
120 Followers 143 Following MSE PhD Candidate & Presidential Fellow @MIT | MechE ‘22 @UCSDJacobs | NSF GRFP | #FirstGen | mechanics & biological materials science 🐎🌱 | she/her
Ricardo @rgarciasandoval
738 Followers 2K Following Phylogeneticist interested on fungi, bioinformatics and old jazz. Teacher at @UNAM_MX ex-AE at #MYCOLOGIA SSC member at @IUCNRedList Plays piano at #Home
keith scovell 💙 @keithscovell3
584 Followers 954 Following Birding, cetaceans, palaeontology, running, biking.All photos mine except RTs. NHS Biomedical Scientist 💙
Necronauta @necronautaa
122 Followers 697 Following ♪ Feminasty🏳️🌈 ♪ I cry a lot but I am so productive, it's an art 🐍
Tonalli @19_illanot
114 Followers 999 Following Just me!, Physics student, 42 . INTJ, 5W4 . Letterboxd: https://t.co/eSBMvLJn2p . Storygraph: tonalli
FershaRuiz @Fersharuiz
462 Followers 342 Following Química, comunicadora de ciencia, curiosa, escritora frustrada, enamorada del saber y de los libros perdidos; con aspiraciones en ciencia. Socia en @LabGeek_mx
Claudia Caba @potrapinta
48 Followers 258 Following Spanish girl/MVZ, Horse lover/Escaramuza. Crines al viento y movimientos armónicos... Two minds one body. 🐎
derek guy @dieworkwear
818K Followers 964 Following Menswear writer. Editor at @putthison. Creator of @RLGoesHard. Bylines at The New York Times, The Washington Post, The Financial Times, Esquire, and Mr. Porter
Giulio Ermanno Pibiri @giulio_pibiri
386 Followers 163 Following Assistant Professor of CS @CaFoscari and Research Fellow @IstiCnr. Indexing, Data Compression, Algorithms.
Laleh Haghverdi @LH33837868
687 Followers 350 Following بيا تا گل برافشانيم و مي در ساغر اندازيم فلك را سقف بشكافيم و طرحي نو دراندازيم
NHS South East Genomi.. @SEgenomics
2K Followers 519 Following Providing genomic testing across South East. Embedding genomics into routine clinical care to enable faster & more accurate diagnoses & personalised treatment.
Olivia Goldman PhD @oliwiagoldman
1K Followers 2K Following Neuro, bioinformatics & chasing my own tail 🤦♀️ | she/her 🏳️🌈 | postdoc, SENse Lab @HHMINews & @UCBerkeley | 🦟 PhD | Co-Founder @cientificolatin 💗 | BLM
Tiago Peixoto @tiagopeixoto
7K Followers 6K Following Statistical mechanic, secular Bayesian. Playing with inferential network science. Associate Professor @dnds_ceu 🦣 https://t.co/gMMpaIoz2V
Valentino Lasso @valentino_lasso
47K Followers 895 Following Artist/Illustrator•✨Characters & Illustrations inspired by 🌿NATURE🌿 Films•Animation•Biology
CamusAltamirano @CamusAltamirano
672 Followers 550 Following Paleoillustrator 🦖, photographer 📷, bass player/vocalist 🎸🎤, Mex 🇲🇽
Robert A. Petit III, .. @rpetit3
2K Followers 2K Following Public health bacterial genomics, bioinformatic workflow development, and training. Bactopia (https://t.co/diBn3GGbqW). @ Wyoming Public Health Laboratory
Laura Gunsalus @lauragunsalus
243 Followers 308 Following Excited about regulatory genomics and deep learning. Bioinformatics grad student at @ucsf in the Pollard and Keiser labs.
Clover Hogan @cloverhogan
9K Followers 536 Following 24yo climate activist | founding Executive Director @fon_xyz | researcher on eco-anxiety | plant burger enthusiast 🌱
Anil Ananthaswamy @anilananth
8K Followers 3K Following Sci journalist/TED speaker/MIT KSJ Fellow/Books: The Edge of Physics, The Man Who Wasn't There, Through Two Doors at Once Mastodon: @[email protected]
Silent @__silent_
10K Followers 197 Following Game developer, modder, reverse engineer, legacy code specialist. I port games for a living and patch them as a hobby. Also known as CookiePLMonster.
Obbe Vermeij @ObbeVermeij
17K Followers 140 Following I make games. Shepherd (Amiga), @SpaceStationSV (N64), @warthegame (steam), @LearniaApp, @GuideApp__ Also: gta3, Vice, SA & IV
James Steele @acier_jean
107 Followers 244 Following Making video games since 1999! Views stated are my own.
ICML Conference @icmlconf
70K Followers 17 Following Int'l Conf on ML • July 21-27, 2024 (Vienna, Austria) • #icml2024 • Contact: https://t.co/6saHKWV01y • https://t.co/sFwmcQNWkE
Anna Riedl @AnnaLeptikon
6K Followers 5K Following nobody. Interested in cognitive science, rationality under radical uncertainty, complexity, systems, insight, meaning, synthesis, wisdom, information design
Mobile DNA @MobDNAjournal
2K Followers 92 Following Mobile DNA is an open access journal that publishes articles providing novel insights into DNA rearrangements in all organisms. #transposon #TE
TEHub @hub_te
843 Followers 288 Following TE Hub is a place where researchers working on Transposable Elements (TEs) can catalog available online resources. https://t.co/I33jkUoblh
Ethan Mollick @emollick
211K Followers 551 Following Professor @Wharton studying AI, innovation & startups. Democratizing education using tech Book: https://t.co/CSmipbJ2jV Substack: https://t.co/UIBhxu4bgq
RECOMB Conference Ser.. @RECOMBconf
1K Followers 248 Following The 28th International Conference on Research in Computational Molecular Biology. April 29 - May 2, 2024
Shiri Gur-Cohen 💔�.. @ShiriGurCohen
2K Followers 662 Following Assistant Professor, Division of Regenerative Medicine @UCSanDiego. Enthusiastic to study how stem cells regenerate our tissues. #NewPI #WomenInSTEM #FirstGen
Nadav Ahituv @NadavAhituv
2K Followers 449 Following Professor, Department of Bioengineering and Therapeutic Sciences, Director, Institute for Human Genetics, UCSF
Mile Sikic @msikic
957 Followers 204 Following Sequence alignment, de novo assembly, algorithms and AI on graphs and strings. Genome Institute of Singapore and University of Zagreb
Yan Holtz @R_Graph_Gallery
19K Followers 723 Following Software engineer who ❤️ #dataviz. Creator of https://t.co/sj29jZPkYr and the R, Python, D3 and React graph galleries. ➡️ https://t.co/PoJNeHXz8a 📈 🌊 🍺
Gael Cristofari @retrogenomics
1K Followers 479 Following Repetitive DNA, Retrotransposons and Genomics, @ircaninstitute, @inserm, @uca_research, @CNRS, https://t.co/dtRRqoTDrJ
Victor Billon @VictorBillon1
399 Followers 582 Following Transposable elements and genes. Mastodon: @[email protected] @retrogenomics lab @ircaninstitute
Victoria @VictoriaParreno
177 Followers 477 Following Former PhD student in @Giacomo_Cavalli's lab at @IGH_MTP, Postdoctoral fellow in @AlejoFraticelli's lab at @IRBBarcelona
Manvendra (Manu) Sing.. @manvendr7
2K Followers 419 Following I research regulatory activities of HERVs in human evo-devo & diseases. Now: Neuroscientist @mpi_nat Alumni: @Cornell @MDC_berlin @ccmb_csir Mostly outdoors!
Akanksha Thawani, PhD @AkankshaThawani
795 Followers 1K Following @DamonRunyon Postdoc @UCBerkeley | Leading Edge Fellow | PhD @Princeton | BTech IITBombay | Transposons, Structural biology and Genome engineering |
Stephanie Eramo @scientiststephe
9 Followers 18 Following PhD Candidate in Structural Biology, Biophysics, and Biochemistry—Ramachandran Lab @4everBiochemist @CUAnschutz
Tim Dunn @T1MD1
209 Followers 341 Following NSF Fellow, PhD Candidate in @UMichCSE at @UMich working on small variant calling accuracy @[email protected]
Hummer Lab @HummerLab
2K Followers 94 Following Molecular simulations and computational biophysics @MPIbp
C3G @C3Genomics
736 Followers 275 Following The Canadian Centre for Computational Genomics (C3G) provides bioinformatics analysis and HPC services for the life science research community.
Guillaume Bourque @guilbourque
3K Followers 589 Following Prof in Human Genetics @McGillU, Director of Bioinformatics @McGillGenome and Director of @C3Genomics @[email protected]
Clément Goubert 🥖.. @clementgoubert
1K Followers 1K Following he/him --- T.E. or not T.E.? 👽🧬 #transposon --- Research Associate @guilbourque lab, McGill, Canada // Mobile DNA+Evolution.
Sam Sternberg @shsternberg
6K Followers 695 Following Assistant professor at Columbia University / CRISPR aficionado / Protein–RNA biochemist / Co-author with Jennifer Doudna of "A Crack In Creation"
Epigenetics Podcast @epigenetics_pod
4K Followers 3K Following @activemotif's epigenetics Podcast hosted by @johndillinger15 #epigenetics #chromatin #podcast | @[email protected] on Mastodon
Bobby Hollingsworth @BobbyHollings
564 Followers 645 Following Postdoc @jwadeharperlab @HarvardCellBio | Ph.D. @BBS_Harvard @WuLabHarvard '21 | @VTEngineering '17 | @bobbyhollingsworth.bsky.social
Miguel Branco @BrancoLab
3K Followers 959 Following Epigenetics and transposons. @brancolab.bsky.social
Christine R. Beck @christinerbeck
1K Followers 768 Following Assistant Professor at The Jackson Laboratory of Genomic Medicine and the University of Connecticut Health Center Views are my own @christinebeck.bsky.social
Poppy Aeron Gould @DrPoppyGould
265 Followers 374 Following Postdoc in @LabRowe at @blizard_inst working on transposons, stem cells and development. She/her. 🏳️🌈
RoweLab @LabRowe
1K Followers 1K Following Immuno-Epigenetics: We study chromatin regulation of tumour immune evasion with the goal to contribute to the discovery of cancer therapies.
Tomás Carrasco @Lupid99
81 Followers 230 Following
Miriam Merenciano @mirimerenciano
241 Followers 285 Following MSCA Postdoctoral fellow at @LbbeLyon. Interested in transposable elements, adaptation, CRISPR/Cas9, drosophilaLinear models makes rough approx to what may be large complex #GRN. Boolean models account for combinatorial complexity but not scalable. scGATE combines #multi_modal info to limit the search space, with better scalability to yield detailed Boolean GRNs doi.org/10.1093/bib/bb…
New reference genomes for two maple species from a combination of Nanopore and Illumina sequencing - including whole genome DNA methylation analysis and associations with long repeat elements and nutrient stress candidate genes by @slmcevoy @JillWegrzyn doi.org/10.1111/eva.13…
New perspective paper: "Aging as a loss of morphostatic information: A developmental bioelectricity perspective" sciencedirect.com/science/articl… @LPiolopez
In academia, no one prepares you for starting a company. I recently had a private talk with UC Berkeley students. Honest and direct about starting a company in Techbio. Including the stuff no one says out loud. Full talk is now live: nfx.com/post/what-i-wi…
Excited to share with the single-cell community the most recent work of @tmontsay and @AEsteveCodina from @cnag_eu, something we think will be a game-changer in #scRNAseq quality control: biorxiv.org/content/10.110… @biorxivpreprint Get ready for the tweetorial! 1/10
@acier_jean You worked on Burnout 3? That's a cool game. Yes, the linear track makes it much easier. But then we were allowed to run in 30 fps with the occasional dip. That wouldn't have been acceptable for you.
@ObbeVermeij Only time I worked on streaming on PS2 was for Burnout 3 - and we had much simpler requirements. We were only ever loading the next track segment, and could start streaming really, really early. Interesting fixes on to slow vehicles down to reign in streaming issues!
It is pretty amazing that the first 1,000 words recovered from the charred scrolls at Herculaneum taught us two new things: where Plato was buried and that he was sold as a slave by the Spartans. Usually, most data you get is boring, a promising start! cnr.it/it/nota-stampa…
Mind blowing 🤯 Transient loss of Polycomb components induces an epigenetic cancer fate | Nature nature.com/articles/s4158…
I'm super excited to share this preprint led by @lahuuki on benchmarking #deconvolution methods vs orthogonal #RNAScope/IF in human brain🧠 in collaboration w/@jhubiostat If you prefer a video version, check Louise's excellent @LieberInstitute seminar 👏🏽 youtu.be/6fTnp_hcYeI
Hey #deconvolution fans! 👀 We’ve got an exciting new pre-print for you: a benchmark of 6 popular deconvolution methods on a multimodal human brain #DLPFC dataset 🧠🧬 @LieberInstitute @jhubiostat #scitwitter 📎 doi.org/10.1101/2024.0…
Massively parallel jumping assay (MPJA). High throughput assay to assess the jumping potential of thousands of retrotransposon sequences/haplotypes. Amazing work by @navneetkmatharu, @JJZhao1203, @KircherLab and many others. biorxiv.org/content/10.110…
I'm thrilled to announce that I successfully defended my PhD thesis today, "Improving select applications of long-read DNA sequencing"! After graduating, I'll be joining @fulcrumgenomics as a Senior Bioinformatics Scientist. I can't wait to see what this next chapter brings!
CLEM-ET data showed that morphologically intact cone-shaped capsids could be found inside the central channel of NPCs and also directly underneath in the nucleus further solidifying that capsids do not need to disassemble for nuclear entry.
If you want to find out more, our preprint is available here: biorxiv.org/content/10.110…
Summarized, our data suggest a nuclear entry model where first a CypA coat around the capsid gets stripped away while the capsid is drawn into the FG-Nup mesh of NPC. Then the compression of the FG-Nups forces the NPC scaffold to crack allowing further progression of the capsid.
In a great collaboration with @HummerLab and the Kräusslich lab, @jpkreysing, @MaziarHeidari1, @VojtechZila and others tackle what happens when HIV capsid goes through an NPC. Instead of the NPC cracking the capsid, the capsid appears to crack the NPC (@MPIbp @CiidHeidelberg).
Totally 🤯 by @shsternberg talk at #ICTE2024: phages have coopted bacterial RNA-guided transposons into RNA-guided transcription factors to precisely manipulate host gene expression! Likely used for inter-phage warfare! biorxiv.org/content/10.110…
Totally wild story by @deMendoza_Alex: DNA methyl transferase unique to Amoebidium unicellular holozoan (sponge-like) silences various endogenous giant viruses and transposons! #icte2024 biorxiv.org/content/10.110…
@samuelruizperez nosotros
Trimming the abstract to 150 words
Amazing to see the work of people in the lab @mirimerenciano #ICTE2024 @ICTE2024
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