Jim Shaw @jim_elevator
Postdoc with Heng Li at Dana-Farber/Harvard Med School. Math PhD from @UofT with @YunWilliamYu. Working on methods for analyzing (metagenomic) sequencing data. jim-shaw-bluenote.github.io Joined April 2018-
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Stunning feat of applied sequencing bioinformatics. Congrats to the authors!!
Stunning feat of applied sequencing bioinformatics. Congrats to the authors!!
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024.0…
skani v0.3.0 is released. github.com/bluenote-1577/… * 30-40% potential reduction in memory * Breaking changes to indexing and searching databases Calculate ANI for contigs, genomes. Search vs > 140k genomes: pre-indexed GTDB-R226 available for download.
I'm excited to share that I will soon join UCLA's Bioengineering department as an Assistant Professor. I am incredibly fortunate to have landed my dream job in this current atmosphere, and I would like to thank my mentors, colleagues, and friends for their support.
Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986
New life update! 🎆 🎓 This Fall, I will be joining the Department of Computer Science at Johns Hopkins University (@JHUCompSci) as an Assistant Professor, with an affiliation at the new Data Science and AI Institute (@HopkinsDSAI).
@csuhuangneng developed longcallR for joint SNP calling and phasing from long RNA-seq reads, AND for identifying allele-specific splicing/junctions (ASJ). Although ASJs of statistical significance are rare, a large fraction involve unannotated junctions. In Rust!
@csuhuangneng developed longcallR for joint SNP calling and phasing from long RNA-seq reads, AND for identifying allele-specific splicing/junctions (ASJ). Although ASJs of statistical significance are rare, a large fraction involve unannotated junctions. In Rust!
GASTON, our method to learn “topographic maps” of gene expression, is out now @naturemethods! IMO the coolest part is a new model of *spatial gradients in sparse data*. As is typical for bio papers, it’s buried in Methods, but see below for a quick outline on the math 👇
GASTON, our method to learn “topographic maps” of gene expression, is out now @naturemethods! IMO the coolest part is a new model of *spatial gradients in sparse data*. As is typical for bio papers, it’s buried in Methods, but see below for a quick outline on the math 👇
Tech Alert! 🚀🧬 We can now determine the sequence of DNA with non-canonical bases in a direct and high-throughput manner with Nanopore sequencing. Check out our preprint for details: biorxiv.org/content/10.110…
Hifiasm 0.21.0 has been released. It now has a beta module for direct assembly of ONT R10 simplex reads. Initial tests with regular simplex reads show very promising results! github.com/chhylp123/hifi…
Happy to see our method for T2T genome assembly published! It addresses an important limitation of string graph, that is, the contained reads. Led by @skamath5e "Telomere-to-telomere assembly by preserving contained reads" doi.org/10.1101/gr.279…
Happy to see our method for T2T genome assembly published! It addresses an important limitation of string graph, that is, the contained reads. Led by @skamath5e "Telomere-to-telomere assembly by preserving contained reads" doi.org/10.1101/gr.279…
Just tried Sylph github.com/bluenote-1577/… by @jim_elevator. Processed >2000 samples in a few hours on google cloud powered by @TerraBioApp. Roughly 15min per sample. Briefly checked the abundances and they match pretty well with what we got using an independent workflow.
I gave a talk recently at Ben Langmead's group on my post on fast computation of random minimizers. Was super fun! Blogpost: curiouscoding.nl/posts/fast-min… Recording: curiouscoding.nl/talks/minimize…
A new paper from our amazing @sladky_on (jointly supervised with @VeselyPavel_mff) on super space-efficient indexing of arbitrary k-mer sets, introducing the Masked Burrows-Wheeler Transform (MBWT).
A new paper from our amazing @sladky_on (jointly supervised with @VeselyPavel_mff) on super space-efficient indexing of arbitrary k-mer sets, introducing the Masked Burrows-Wheeler Transform (MBWT).
bl @xbodus
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Estella @Irbawirwui3135
38 Followers 2K Following She shines not because she wants to be seen, but because she cannot help it.
Xiaojun SU @Xiaojun_SU1
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Jia-Xing Yue (岳家�... @iAmphioxus
689 Followers 2K Following PI of @EvomicsLab at Sun Yat-sen University Cancer Center (SYSUCC) Alumni of @CNRS @ircaninstitute @RiceUniversity @NanjingUnivers1
Chris Seymour @iiSeymour
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Meghana Srinivas @meghana_srini
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Daniel Tabin @DanTabin
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Aoxing Liu @Aoxing2
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David Allegakoen @DAllegakoen
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Alex (Chen Zhang) @Tsins361158385
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Michal Tal, PhD @ImmunoFever
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ONLYTRADES @0nlyTrad3s
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J. Antonio Baeza @J_Antonio_Baeza
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stewir @Nuozoot
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Saubashya Sur, PhD @SaubashyaSur
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Yosuke Nishimura @ysknishimura
690 Followers 610 Following メタゲノムデータをフル活用した微生物の研究をしています。海洋研究開発機構研究員 Researcher in JAMSTEC. Metagenomics and bioinformatics.
Anatoly @t2v12
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Li Xuemei @KristinLaw69044
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Huang Qichang @TaTzung50896
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Akshaya Vasudevan @vasuakshaya15
75 Followers 553 Following PhD candidate at the University of Ottawa. Agriculture and Agri-Food Canada.
Nicholas Ollberding @Nick10243
86 Followers 203 Following Associate Professor @CincyChildrens Epidemiology|Microbiome|Biostatistics|Predictive Modeling|Views are my own
Yosuke Tanigawa @yk_tani
2K Followers 1K Following Assistant Professor, UCLA Bioengineering. Research: disease heterogeneity dissection.
Amira @AmiraVCPH
667 Followers 882 Following Interests in #bacteriophages, microbiology, bioinformatics, pathogenic bacteria and #antibioticresistance Also, plants and fungi
Joshua Cooper @jthomascooper
402 Followers 2K Following Phycologist, Diatoms, Aquatic and Microbial ecologist, and dabbler of bioinformatics. Associate Professor Northern Kentucky University. Tweets are my own.
Dr Rob Leigh @RobLeigh_
609 Followers 2K Following Research Fellow in Bioinformatics & Molecular Epidemiology @TrinityMed1. Adj Asst Prof in Stats @SETUIreland. Interested in omics based approaches to medicine
Rasmus Kirkegaard @kirk3gaard
3K Followers 626 Following Staff scientist having fun with DNA seq and bioinformatics at #AlbertsenLAB. 🦋@kirk3gaard.bsky.social. COI : I am a @nanopore shareholder.
Pengfei Yin @Pengfei_Yin_
14 Followers 450 Following Genome assembly | Computational epigenomics (3D genome) | Physics (explain biological phenomena) | BSc @OUC1924 I MSc @SUSTechSZ
Dr Stella Loke @LokeStella
817 Followers 675 Following Human, multiparous, science nerd, runner #NGS #Genomics [email protected]
Jonathan Haars @JonathanHaars
86 Followers 608 Following Phd-student and laboratory technician at Uppsala University Hospital/Uppsala University Working with #SARSCoV2, #Metagenomics, #NanoporeSequencing
Ryan Wick @rrwick
3K Followers 389 Following No longer active here. Find me on Bluesky: https://t.co/1mPtWVlnli
Yuya Kiguchi, PhD @YuyaKiguchi
130 Followers 404 Following PostDoc @ Stanford Univ. ← PostDoc @ Univ. of Tokyo ← PhD @ Waseda Univ. Microbiome, Metagenome.
Bao-Tran N. Le @dauphongpiupiu
2 Followers 129 Following
Jin Seok (Andy) Lee @iam_js_lee
176 Followers 490 Following PhD candidate in bioinformatics & computational biology @pirl_unc | Long-read sequencing | Neoantigen discovery
Yiyuan Li (YY) @yy_yiyuan_li
522 Followers 1K Following Postdoc in Moran lab at UT Austin. Interested in Host-symbionts Interactions, Coevolution Between Genomes, Insect Genomics, Environmental DNA. He/him
Takumi Otagaki @OtagakiTakumi
47 Followers 125 Following University of Tokyo. M2. Bioinformatics. 学振合格お祈り中. jazz guitar 🔰
GigaScience @GigaScience
10K Followers 10K Following The #OpenScience journal from BGI & OUP publishing articles using/generating large datasets. And linked to @Giga_DB #opendata hosting/analysis repository
André Soares @GeoMicroSoares
2K Followers 5K Following 🇵🇹 Staff scientist at the @ProbstLab @unidue doing all kinds of fun science! Once did a PhD at #faberystwyth 🏴
Yangzhen Li @LiYangzhen
115 Followers 596 Following Associate Prof in aquaculture genetics and genomics. Love to teach fishing, rather than giving fish.
Sara Bakić @sarrabakic
67 Followers 146 Following PhD student at @NUSingapore, @astar_gis | Bioinformatics | NLP | ML
Roland Ewald @rlndwld
224 Followers 871 Following Co-founder @limbusmedtec, working on clinical #genomics platform #varvis. (Views my own.)
ya bo1 money @yabo1money
92 Followers 1K Following trying to put your genes in your jeans Salivaomics over Hematology
Ashley Jones @dnawhisperer
363 Followers 615 Following Post-doc @BiologyANU @PlantSci_ANU. Plant and fungi genome biology, transcriptomics, epigenetics, long-read sequencing, bioinformatics 🍃🧬🔬🧋
Ryan Reis @Ryan_J_Reis
257 Followers 1K Following Jabbari Lab @ Carver College of Medicine MSTP M6G | Cancer, Bioinformatics, Immunology, Translational #singlecell #omics #Research
Marcin Cieslik @i000
384 Followers 3K Following
Yosuke Tanigawa @yk_tani
2K Followers 1K Following Assistant Professor, UCLA Bioengineering. Research: disease heterogeneity dissection.
Pengfei Yin @Pengfei_Yin_
14 Followers 450 Following Genome assembly | Computational epigenomics (3D genome) | Physics (explain biological phenomena) | BSc @OUC1924 I MSc @SUSTechSZ
Siddarthan Venkatacha... @Venkatachalam4
584 Followers 2K Following Engaged in #microbialecology and #genomics research from alpine to polar environments. Project Scientist-II at NCPOR, Goa, India
Adam Vivian-Smith �... @phylogenypluckr
840 Followers 6K Following scientist+ dad (son w. trisomy21 +ASD) | interests; plant reproduction, genetics, ∞evolution, paleobotany seedplants auxin RNA fruitset genomics/bioinformatics
Jonathan Haars @JonathanHaars
86 Followers 608 Following Phd-student and laboratory technician at Uppsala University Hospital/Uppsala University Working with #SARSCoV2, #Metagenomics, #NanoporeSequencing
Tony Tu @Qwe1029384756Tu
152 Followers 434 Following PhD candidate in Machine Learning @ Georgia Tech, former intern @ Meta, former researcher at UC Berkeley BAIR lab Generative AI & Protein Design at Georgia Tech
Doukeshi @UK_intelli_GENT
131 Followers 1K Following Be less curious about people and more curious about ideas.” – Marie Curie #science #microbiology #technology #gaming #anime #intelligent #games #tattoos
Dylan Duchen @DylDuch
376 Followers 2K Following Genetic Epidemiology + Computational Immunology Postdoc with @skleinstein , @Yale-@Boehringer Fellow | Previously: Genetic Epidemiology @JohnsHopkinsSPH
André Soares @GeoMicroSoares
2K Followers 5K Following 🇵🇹 Staff scientist at the @ProbstLab @unidue doing all kinds of fun science! Once did a PhD at #faberystwyth 🏴
Roland Ewald @rlndwld
224 Followers 871 Following Co-founder @limbusmedtec, working on clinical #genomics platform #varvis. (Views my own.)
Takumi Otagaki @OtagakiTakumi
47 Followers 125 Following University of Tokyo. M2. Bioinformatics. 学振合格お祈り中. jazz guitar 🔰
Rasmus Kirkegaard @kirk3gaard
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naturepoker @naturepoker1
2K Followers 1K Following Amateur biologist at Binomica Labs. Phage hunting. #amateurbiology @[email protected] https://t.co/dvUy3KczVN https://t.co/zAFupGZgMp
Anders B. Dohlman, Ph... @abdohlman
54 Followers 403 Following Postdoc & Damon Runyon Fellow in Matthew Meyerson’s lab @DanaFarber @broadinstitute, @harvardmed. I study genomics & host-microbe interactions in cancer.
Johanna von Wachsmann @vWachsmann
53 Followers 129 Following PhD student at EMBL-EBI and the University of Cambridge
Kenya Honda @Honda1Kenya
413 Followers 93 Following I'm a Professor at Keio University School of Medicine in Tokyo studying the impact of the human gut microbiome on immunity, metabolism, and healthy longevity.
Hasindu Gamaarachchi @Hasindu2008
1K Followers 1K Following Lecturer at UNSW Sydney; Visiting Scientist at Garvan Institute of Medical Research - Designing embedded systems for bioinformatics applications.
Emily White @emc_white
947 Followers 392 Following Microbiologist 🦠 Chief editor @NatureMicrobiol 📚 Views my own
Luis E. Valentín-Alv... @luisarchaeota
3K Followers 3K Following microbial genomics, enzyme function research fellow @hfsp at @MonashBDI | microbial genomics PhD from @Banfieldlab @savagecatsonly at @UCBerkeley #firstgen
Nick Minor @itsnickminor
1K Followers 1K Following Bioinformatician & data scientist working on host and pathogen genomics. Writing in Python, R, Rust, Nextflow, and more.
Clement Tsui 徐健�... @km_tsui
950 Followers 2K Following Prin Scientific Officer, IDRL/NCID, Singapore; aff. AProf @UBC; views are my own; #genomics #evolution #ecology #fungi 🇭🇰 🇨🇦 @[email protected]
Maximillian Marin @maxgmarin
561 Followers 2K Following Researcher studying genomics and infectious disease at Harvard Medical School.
Aaron Pomerantz, PhD @AaronPomerantz
6K Followers 2K Following Associate Director, Global Segment Marketing @nanopore. Micro/Infectious/Synthetic Bio. The coolest discoveries are the ones you make. Tweets/views are my own.
Greg Medlock @MedlockGreg
140 Followers 434 Following Sr Director R&D @vedantabio. Interested in drug development, infection prevention, microbiome, systems biology, & urban policy. On Bsky now.
Sudaraka Mallawaarach... @sudaraka_m
285 Followers 1K Following Marie-Curie Fellow. Researcher in pathogen genomics @PeterMacRes @UniOslo @OCBE_UniOslo @UniMelb previously @MelbIntGen - he/him
R. Eric Collins @rec3141
1K Followers 4K Following Canada Research Chair in Arctic Marine Microbial Ecosystem Services at the University of Manitoba
Richard Allen White I... @raw9371
966 Followers 346 Following Assistant Professor of Bioinformatics and Genomics at UNCC. Computational and Molecular Virologist. Passionate about the eradication of pathogens. #rawlab #uncc
Natsuko Hamamura @nhamamura
194 Followers 227 Following Professor in microbial ecology, microbe-mineral interactions, bioremediation, @KyushuUniv_EN @oregonstatealum #geomicrobiology #microbialecology #WomenInSTEM
Daniel Gregoire @DanielSGregoire
921 Followers 913 Following Metals, Microbes, and the Environment | Assistant Professor at Carleton University | Co-founder of Microbright
Jeremy Wilkinson @jewilki
593 Followers 1K Following Molecular bio, microbiome, metagenomics, runner, sports, food & drink, camper, @okstate & @texastech alum, formerly @hutlab @harvard, now @PacBio. Views my own
Judit Burgaya @juditburgaya
546 Followers 1K Following PhD student in computational modeling of bacterial populations, microbial genomics, AMR evolution | Twincore - Hannover Medical School and HZI | Roller hockey
James Docherty @JamesDoc93
728 Followers 741 Following Postdoctoral researcher in the @SashaZhernakova Lab at University Medical Center Groningen. Former PhD student with @EvelienAdri at @TheQuadram 🦠
William Chow @wchowb
336 Followers 405 Following A UK based Bioinformatician/Canuck at @Basecamp_Res . Prev @SangerInstitute + @Genomeref, @darwintreelife, @genomeark, @EBPgenome. Views my own.
Qiyun Zhu @zhuqiyun
211 Followers 228 Following Assistant Professor @ASU | Studying #microbiome, #evolution, #bioinformatics, #multiomics | Developing scikit-bio (https://t.co/aXG7aMZ0Nc) | Open-source enthusiast
Tyler Barnum, Ph.D. @tylerbarnumphd
743 Followers 491 Following Sr. Scientist, Computational Biology @CultivariumFRO. Prev. @tracegenomics & PhD @PMB_Berkeley. Tweets about microbio, genomics, and halogens
Quan Ton Ngoc Minh @quanntnm
83 Followers 1K Following currently working on human microbiome, using @nextflowio to create scalable and reproducible pipelines
Simon Roux @simroux_virus
4K Followers 2K Following Virus-obsessed 🇫🇷 bioinformatician, DOE JGI Scientist, Having fun with #metagenomics and other cool #omics. He/him. Opinions my own. simrouxvirus on bsky
Nature Biotechnology @NatureBiotech
319K Followers 2K Following Publishing the best of biotech science and business. Find us on Bluesky, Facebook & Instagram. Part of @SpringerNature and @NaturePortfolio.
Guillaume GAUTREAU @GUILLAUMEGAUTRE
367 Followers 755 Following PhD in #CompBio. (Meta/Pan)genomics. Health Law. GDPR compliance. https://t.co/DgYQbHZTYl… @INRAE_France scientist at @INRAE_MaIAGE. @[email protected]
UBC Dept of Microbiol... @UBCMicroImmuno
2K Followers 562 Following The Department of Microbiology and Immunology @ubcscience @UBC https://t.co/Thq2FmZNw9 Bluesky: https://t.co/wnG8YXCQRB
Brice Letcher @bricoletc
342 Followers 333 Following --On blu*sky-- Researcher in biology, bioinformatics, evolution, genomics. PhD @emblebi/ @cambridge_uni (malaria); postdoc @ENSDeLyon (nematodes)Trends for United States
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