thecodingbiologist @codingbiologist
Creating tools and tutorials to make lab life a little easier. thecodingbiologist.com Joined December 2021-
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Following314
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Excited that our work on transcription-coupled DNA repair is now published @CellCellPress! We recapitulated TC-NER in Xenopus egg extract and identified STK19 as a core repair factor that couples stalled Pol II to TFIIH. 🧬🐸 ➡️ cell.com/cell/fulltext/…
Make publication ready figures from your #AlphaFold PAE files. Works on multimer and AlphaFold 3 files. Customize colors and export as an SVG for editing in illustrator! thecodingbiologist.com/tools/pae.html
Excited to share that our new preprint is out! We used #AlphaFold multimer to screen 7000+ nuclear proteins to find new nucleosome acidic patch binders. Great collaboration between @FrogWalterLab and @LucasFarnung. biorxiv.org/content/10.110…
Riding the #AlphaFold3 wave with a new analysis tool. It’s super new/unpolished, but would love to get community feedback! Extract and filter residue level interaction data from your AF3 server prediction zip files! Try it here: predictomes.org/tools/af3/
So excited to share the first work from our lab. Led by @StevePilley with help from lots of amazing collaborators. A special shout out to @LyssiotisLab and @BKennedy_aging and their labs!
Introducing the SPECTRA python package! github.com/mims-harvard/S… This package implements the spectral framework for model evaluation. All you need to get started is (1) a model, (2) a dataset, and (3) a definition of sample to sample similarity!
Introducing the SPECTRA python package! github.com/mims-harvard/S… This package implements the spectral framework for model evaluation. All you need to get started is (1) a model, (2) a dataset, and (3) a definition of sample to sample similarity! https://t.co/c7thjGFTtB
I just posted the first of what will be several chapters about transformers, which in the last year has been the most requested topic for the channel. youtu.be/wjZofJX0v4M
couldn’t agree more about the need for more computational biologists. More importantly, we must ensure they receive the recognition and support they deserve. Their work should never be dismissed as merely “just service”. Additionally, I’d like to remind everyone of the excellent…
couldn’t agree more about the need for more computational biologists. More importantly, we must ensure they receive the recognition and support they deserve. Their work should never be dismissed as merely “just service”. Additionally, I’d like to remind everyone of the excellent… https://t.co/7f7sxXIWR6
Check out this massive study led by @GygiLab member Jonathan Van Vranken and lab alumnus @dschweppe1 to learn how thermal stability measurements and small molecule screening can be used together to tease apart the compounds' direct and indirect effects!
Check out this massive study led by @GygiLab member Jonathan Van Vranken and lab alumnus @dschweppe1 to learn how thermal stability measurements and small molecule screening can be used together to tease apart the compounds' direct and indirect effects!
Our essay in Nat Cell Bio: "Bringing computation to biology by bridging the last mile" We argue to shift resources/rewards towards creating user-friendly software to bridge computation and biology-it yields huge returns! @shantanuXsingh Free author link: rdcu.be/dv82F
A higher power
Stringz: A GUI based string manipulation tool producthunt.com/posts/stringz via @ProductHunt
Analyze strings, reveal hidden characters, visualize character indices and more: thecodingbiologist.com/tools/chartool…
Drop an #AlphaFold PDB file, select the chain and or region you want to analyze, and export the pLDDT values. It's that easy: thecodingbiologist.com/tools/plddt.ht…
I’m looking for a postdoc who wants to work with me and Andrew Kruse to design and characterize new protein sensors! If you’re interested or have any leads, let me know!
I had a great time working with the @GygiLab team on this story! GoDig is an amazing new tool that allows for rapid targeted proteomics assay development. Congrats to Qing and everyone involved. Check it out ⬇️ nature.com/articles/s4146…
Twixep @Twixep190222
1 Followers 784 Following
Consortium for Top-Do... @TopDownProteome
2K Followers 2K Following Collaboration, education, and innovative research accelerating the comprehensive analysis of all human proteoforms. https://t.co/BNhhb78Wdk https://t.co/pTAjgMwCEh
Jonas @JohannJRoske
97 Followers 177 Following PhD student @MRC_LMB @Yeeles_Lab studying DNA replication using structural biology.
Andrey Feklistov @AndreyFeklistov
98 Followers 524 Following BioChem & StructBio | transcription person | SBDD | Stanford/BioTech | dog dad 🏳️🌈
MargotGalle @MARabidopsis_
30 Followers 100 Following Here for the science: falling down the literature rabbit hole and trying to fit crazy research ideas into a single PhD!
Binita Shah @binitashahah
64 Followers 147 Following Ph.D. Candidate at @harvardmed. Co-mentored by Eric Fischer and Sara Buhrlage. NIH NCI F31 recipient.
Ryan Murray, PhD @rcm181
193 Followers 468 Following Co-Founder/CSO @KiraGenBio. On a quest to harness the power of the immune system to solve complex problems in human health
Aaron Edwards @aedwards02
1K Followers 2K Following Co-Founder/CEO @KiraGenBio | MS/MBA @HarvardHBS | Past CAR-T editing @beamtx & @bluebirdbio.
LudicrousLily @LilyLudicr4247
2 Followers 118 Following
Keith Connolly @KeithMConnolly
46 Followers 356 Following
Primavera @terirough51230
22 Followers 552 Following The night is coming, I'll be waiting for you on the air. https://t.co/6E7lzmiNt8
Maria Gonçalves @Maria_CBG
123 Followers 315 Following Neuroscientist & Public Health advocate. Music-botanic-philosophy lover. @WyssInstitute | @HarvardMed | @geochurch lab #NeuroImmunology #Aging
Patrick Murphy @metablab_upei
264 Followers 522 Following Asst. Prof. @UPEI_Biology @UPEI. Adjnct Prof. @Dal_Pathology. Assoc. Memb. @BHCRI. Interested in metabolite and protein function in cells. Tweets are my own.
Dr. Erin Baker @ErinBakerIMS
5K Followers 4K Following Farm girl turned scientist and interested in anything mass spec :) Also, Associate Professor @uncchemistry.
plasmidsaurus @plasmidsaurus
11K Followers 10K Following Pioneers in the sequencing of whole plasmids, amplicons, whole bacterial genomes & more. 900+ dropboxes and 10 labs globally.
Jesper V. Olsen @jespervolsen
1K Followers 1K Following
Gary Siuzdak @kadzuis
6K Followers 5K Following Scientist, heal thyself. Designing #METLIN & #XCMS to identify active natural products, lipids, metabolites, drugs… https://t.co/WtRlKrV5Zs
Ray Wang @rayneurobio
18 Followers 369 Following
Sophie @SophieRth98
43 Followers 149 Following PhD at Harvard & LMU, studying #transcription // #BIF PhD Fellow // either shooting 📸 or pipetting 🧪🧬 // website below 👇🏽
J E Soto @e_sotog
210 Followers 1K Following
Bailey Schultz @bjschul7
534 Followers 1K Following Ph.D. candidate in the Walker Lab @chemical_phd. Former @Sattely_lab member. He/him. 🏳️🌈
Dr. Joyce Lee @Joyce_Lee_91
341 Followers 194 Following Scientist @ Vertex Cell and Gene Therapy | Post Doc training in Walter & Pellman labs @ HMS/DFCI | PhD from Berger lab @ JHMI
Kit Lewers @KitLewers
210 Followers 549 Following Info Science and Quantitative Biology PhD’ing at CU working with NASA BioSCape currently, Software & Database Engineer at Planning Pod 🦬 🪲🛰️💻
Kẹnịtimi Biikịk... @Kenitimi
333 Followers 1K Following Rich Nigga, Poor Nigga, Field Nigga, House Nigga, Still Nigga!
Benjamin Angulo @Bangulo89
93 Followers 347 Following PhD Student at @geochurch lab at @wyssinstitute/@Harvard, Dept of Genetics. Previously Managing Director of Nucleate Boston
cx @QriusScientist
1 Followers 66 Following
Lucas Farnung @LucasFarnung
3K Followers 270 Following Assistant Professor @HarvardCellBio. Transcription & Chromatin; Biochemistry, X-ray & Cryo-EM. Views are my own.
Ana Rivas @rivas_arias_
24 Followers 199 Following 1st year graduate student @NU_Chemistry • Proteomics • Mass Spec
Lisa Boatner @lisa_boat
124 Followers 367 Following computational scientist & chemical biologist @UCLA 🏔️ hiker | 🧗🏻♀️climber | 🎨 artist | 🤘🏻alum @UTAustin
Fata @callmefataa
2 Followers 25 Following
Yolanda Markaki @YolandaMarkaki
109 Followers 336 Following Group leader @LeicStructBio Nothing beyond the nucleus-the cytoplasm? nuclear organisation, epigenetics, X inactivation, super-resolution microscopy, cats&dogs
Fariba @Fariba19944
131 Followers 520 Following MSc Genetics🧬 | researcher 👩🔬 | interesting in genetics molecular cancer, biotechnology, bioinformatics | yogini girl🧘🏼♀️
Steven Pilley @StevePilley
286 Followers 948 Following Hi I’m Steve and I’m a scientist. Postdoc in the Mullen lab @USC. Fulham fan.
Amy Tam @amyyxt
122 Followers 2K Following computational systems biologist 🧬 EDI advocate in STEM, medicine, healthcare 👥 philosopher 💬 food-security organizer 🧺 future physician-scientist 🧑🏻⚕️
Brandon Chen, PhD @BrandonTWChen
1K Followers 2K Following @theNCI K00postdoc with @KivancBirsoy |PhD with @Lyssiotislab & @Yatrikshahlab | organelle & metabolism 🌈
Andrea Brighi 🇪�... @Anbri1799
21 Followers 319 Following medical student. aspiring physician-scientist. pro-progress
Juanma Schvartzman @Schvartzman_JM
1K Followers 2K Following metabolism + chromatin biologist #chroMetab, GI medonc @columbiacancer and dad | 🇪🇸🇵🇾🇦🇷🇺🇸 | @schvartzman.bsky.social | @[email protected]
Mychael Lourenco @mvlourenco
3K Followers 2K Following Neuroscientist studying molecular mechanisms of Alzheimer’s disease and related disorders. Assistant Professor at @UFRJ.
Karan Singh @_nameinframes_
15 Followers 40 Following
Costas Chronis @ChronisLab
83 Followers 175 Following
Izzy Hunsberger @izzy_hunsberger
26 Followers 53 Following PhD student at The University of Idaho ~ Microbiology, Molecular Biology, & Biochemistry; B.S. in Molecular & Cellular Biology (Penn State University, 2019)
Sivaprasad @ps_sivaprasad_
115 Followers 984 Following BS-MS'24 👨🏻🎓 @IISERPune| KVian'18🏫| Native Kochi🏞️
Jane Liu @jane_yliu
163 Followers 443 Following PhD candidate @harvardmed, Sarah Fortune Lab @HarvardChanSPH | Bryn Mawr College ’17
Yadong_Qi @Yadong_Qi
18 Followers 653 Following
Victor Lau @Vzplau
141 Followers 493 Following Iterating Nested Frameworks; 🤝 Increase Connecting, Not Attachment. Repurposing Senescence to Elucidate the Brain. Views my own, he/him
Talal Hossain @talal_hossain
416 Followers 3K Following #Phages #NewDad ❤️ #RoslinInstitute #University of Edinburgh #WellcomeTrustSangerInstitute #UniversityofCambridge #icddrb #Bangladesh
Jörg Stülke @JorgStulke
2K Followers 256 Following #bacillus #subtiwiki #MiniBacillus @Bacell_EU @Rafts4Biotech @SPP1879 @UniGoettingen
Christoph Elfmann @c_elfmann
101 Followers 63 Following @IMPRS_GS PhD student in bioinformatics at the @JorgStulke lab of @UniGoettingen, currently working on SubtiWiki's newest iteration
Lori Passmore @lapassmore
5K Followers 807 Following Molecular biologist. Group Leader @MRC_LMB. Fellow @clarehall_cam. Optimist. (she/her) Views/opinions are my own.
MargotGalle @MARabidopsis_
30 Followers 100 Following Here for the science: falling down the literature rabbit hole and trying to fit crazy research ideas into a single PhD!
owl @owl_posting
11K Followers 802 Following technical staff @noetik_ai || ex ml eng @dyno_tx || i write/podcast about bio ml at https://t.co/QPTHsR3fzm || art on https://t.co/SwGiuSjlXF
Binita Shah @binitashahah
64 Followers 147 Following Ph.D. Candidate at @harvardmed. Co-mentored by Eric Fischer and Sara Buhrlage. NIH NCI F31 recipient.
Golgi Graphics @GolgiGraphics
467 Followers 83 Following Scientific illustration services for academia and biotech | Pairing scientific accuracy with engaging design | Figures, infographics, 3D animation.
Ryan Murray, PhD @rcm181
193 Followers 468 Following Co-Founder/CSO @KiraGenBio. On a quest to harness the power of the immune system to solve complex problems in human health
Aaron Edwards @aedwards02
1K Followers 2K Following Co-Founder/CEO @KiraGenBio | MS/MBA @HarvardHBS | Past CAR-T editing @beamtx & @bluebirdbio.
Yasha Ektefaie @YEktefaie
610 Followers 800 Following Bioinformatics PhD Student @HarvardDBMI | @UCBerkeley 2020 graduate in @BerkeleyBioE + @Berkeley_EECS | Fan of movies, music, and running!
Andrea Vettiger @AVettiger
546 Followers 418 Following Assistant Professor @DMF_UNIL Postdoc Bernhardt lab | PhD Basler lab. Shining light on small bugs to reveal their amazing biology! #elongasome #divisome #T6SS
Andrew Cicchetto @CicchettoAndrew
15 Followers 116 Following
Lisa Boatner @lisa_boat
124 Followers 367 Following computational scientist & chemical biologist @UCLA 🏔️ hiker | 🧗🏻♀️climber | 🎨 artist | 🤘🏻alum @UTAustin
Ana Rivas @rivas_arias_
24 Followers 199 Following 1st year graduate student @NU_Chemistry • Proteomics • Mass Spec
Kit Lewers @KitLewers
210 Followers 549 Following Info Science and Quantitative Biology PhD’ing at CU working with NASA BioSCape currently, Software & Database Engineer at Planning Pod 🦬 🪲🛰️💻
J E Soto @e_sotog
210 Followers 1K Following
Amanda Jayne Collier @Mandy_Collier
409 Followers 709 Following Postdoc fellow @UCLA @PlathLab | Alum @Cambridge_Uni @BabrahamInst | Researching epigenetic changes during human embryonic development
Tat1anaMoiseeva.bsky.... @Tat1anaMoiseeva
1K Followers 666 Following see you on 🦋🟦 Assistant Professor at the University of Pittsburgh. Opinions are my own.
NVIDIA Healthcare @NVIDIAHealth
12K Followers 146 Following The official handle for #NVIDIAHealthcare. Helping the scientific and developer community advance research, diagnostics, and patient care with #AI.
Aparna Bhaduri @BhaduriLab
1K Followers 739 Following Assistant Professor at UCLA in the Department of Biological Chemistry
Aleph Alpha @Aleph__Alpha
9K Followers 1 Following Our mission is a European generalizable AI. We're hiring: https://t.co/k7MxJK1XU1 #AGI, #artificialintelligence, #writtenbyahuman,#writtenbyanAI
Keith Connolly @KeithMConnolly
46 Followers 356 Following
Maria Gonçalves @Maria_CBG
123 Followers 315 Following Neuroscientist & Public Health advocate. Music-botanic-philosophy lover. @WyssInstitute | @HarvardMed | @geochurch lab #NeuroImmunology #Aging
Alex Chu @alexechu_
2K Followers 747 Following Deep learning & protein design. @googledeepmind PhD @Stanford
Faisal Mahmood @AI4Pathology
6K Followers 2K Following Associate Prof. @Harvard | Faculty @harvardmed @MassGenBrigham @broadinstitute @harvard_data | Multimodal, Generative, & Agentic AI for Biomedicine
Vousden Lab @LabVousden
3K Followers 144 Following We study intrinsic cancer cell metabolism, crosstalk between tumour and stroma in TME, and the interplay between cancer and systemic conditions @theCrick
Agata Smogorzewska @MaintainGenome
2K Followers 346 Following The Laboratory of Genome Maintenance at the Rockefeller University studies genetic diseases to understand how DNA repair prevents cancer development and aging.
Alex Rives @alexrives
10K Followers 906 Following AI for scientific discovery. Broad and MIT. Chief scientist at @EvoscaleAI and founder and scientific director of the ESM project previously @Meta.
Primordium @PrimordiumLabs
2K Followers 1K Following The world’s best academic labs and top biotech companies rely on us every day for overnight whole-plasmid and PCR sequencing.
Ali Madani @thisismadani
7K Followers 1K Following Founder & CEO of Profluent (https://t.co/GpoVdKW1zQ, we're hiring!). AI+Biology to cure disease. Berkeley PhD. formerly Research @ Salesforce AI.
Roger Greenberg @RogerRogergr
3K Followers 2K Following The Greenberg lab investigates processes that affect genome integrity and how they influence human biology
Scientific Python @SciPyTip
210K Followers 18 Following Tweets about SciPy (Scientific Python) and related topics from @JohnDCook.
Patrick Murphy @metablab_upei
264 Followers 522 Following Asst. Prof. @UPEI_Biology @UPEI. Adjnct Prof. @Dal_Pathology. Assoc. Memb. @BHCRI. Interested in metabolite and protein function in cells. Tweets are my own.
Machine learning for ... @ml4proteins
8K Followers 122 Following Seminar series on machine learning for protein engineering. Details for seminars and slack are on our website. DM us if you're interested in presenting!
QIAGEN Life Sciences @QIAGENscience
10K Followers 2K Following Learn more about Sample to Insight solutions for PCR/qPCR, NGS and automation in life sciences. Visit https://t.co/fEdXt328P0
Martijn Luijsterburg @luijsterburglab
2K Followers 439 Following The Luijsterburg lab at the LUMC in Leiden investigates DNA repair mechanisms during gene transcription.
plasmidsaurus @plasmidsaurus
11K Followers 10K Following Pioneers in the sequencing of whole plasmids, amplicons, whole bacterial genomes & more. 900+ dropboxes and 10 labs globally.
Mohammed AlQuraishi @MoAlQuraishi
11K Followers 350 Following MLing biomolecules en route to structural systems biology. Asst Prof of Systems Biology and CS @Columbia. Prev. @Harvard SysBio; @Stanford Genetics, Stats.
Karlene Cimprich @KarleneCimprich
2K Followers 53 Following
MLSB (in San Diego + ... @workshopmlsb
2K Followers 0 Following Machine Learning in Structural Biology workshop co-located with NeurIPS 2025 & at EurIPS 2025. Dec 7. San Diego, CA
AI Proteins @AI_Proteins
3K Followers 29 Following better medicines, created rapidly through de novo protein design
Alexey Nesvizhskii @nesvilab
5K Followers 292 Following Godfrey D. Stobbe Professor of Bioinformatics at U of Michigan. Trained as a theoretical physicist, now focusing on proteomics and proteogenomics.
Gary Siuzdak @kadzuis
6K Followers 5K Following Scientist, heal thyself. Designing #METLIN & #XCMS to identify active natural products, lipids, metabolites, drugs… https://t.co/WtRlKrV5Zs
Dr. Erin Baker @ErinBakerIMS
5K Followers 4K Following Farm girl turned scientist and interested in anything mass spec :) Also, Associate Professor @uncchemistry.
Jesper V. Olsen @jespervolsen
1K Followers 1K Following
Oliver M. Bernhardt �... @OliverMBernhar1
1K Followers 118 Following Lead Developer of Spectronaut @Biognosys (since 2011). Wrote analysis algorithms for DIA, DDA, PRM, MRM, PASEF, FAIMS, BoxCar, PTMs and more.
Rob Moritz @r_l_moritz
1K Followers 620 Following Head, Proteome Research, Prof at the Institute for Systems Biology (ISB) @ISBsci. Past Chair-Human Proteome Project , Human Proteome Org https://t.co/25bLL02wul
New England Biolabs @NEBiolabs
10K Followers 967 Following Developing innovative products for the life science industry and providing insightful technical support. Community guidelines at https://t.co/KhEztOwYcaTrends for United States
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