Reposted by Bernardo Pinto Arne Elofsson @handle.invalid · 08/09/2026www.nature.com/articles/d41...nature.comOpenAI claims huge maths breakthrough on a famed ‘Millennium Problem’The company says it has cracked the physics of fluids using AI, solving one of the toughest puzzles in mathematics. 002 2
Reposted by Bernardo Pinto Roland Dunbrack 🏳️🌈 @rolanddunbrack.bsky.social · 27/06/2026I think @biorxivpreprint.bsky.social is having a bad day. 001 1
Reposted by Bernardo Pinto Leonid Schneider @forbetterscience.bsky.social · 22/06/2026What exactly is this, dear @acs.org ? pubpeer.com/publications... 062 6
Reposted by Bernardo Pinto Arne Elofsson @handle.invalid · 10/05/2026idp.nature.com/authorize?re...idp.nature.comRevealed: the mysterious ‘dark’ proteins that might play a big role in biologyThousands of dark proteins have been reclassified as peptideins and added to databases as a new category. 031 3
Reposted by Bernardo Pinto Elisabeth Bik @elisabethbik.bsky.social · 08/05/2026Fabricated citations: an audit across 2·5 million biomedical papers The fabrication rate increased more than 12 times between 2023 and early 2026. Possible causes: Paper Mills, AI use etc www.thelancet.com/journals/lan...thelancet.comFabricated citations: an audit across 2·5 million biomedical papersScientific literature depends on the integrity of its references. Each reference implicitly asserts that a verifiable source exists and supports the claims being made. When references point to non-exi... 26629 66
Reposted by Bernardo Pinto Commercial Solar Guy @commercialsolarguy.com · 02/05/2026I think this is why you don’t use water on battery fires… 1012538 125
Reposted by Bernardo Pinto Cordero-Vásquez Lab @cvlab.bsky.social · 27/03/2026Excited to share our new paper in Science Advances @science.org In this work, we uncover how a disease-linked TRPC3 mutation, together with a cerebellum-specific splice isoform, stabilizes the channel in an open state, drives Calcium overload, and promotes neurodegeneration. (1/4)science.orgFunctional and structural basis of a hypermorphic TRPC3 variantStructural snapshots capture an ataxia-linked overactive ion channel in its open state and reveal a druggable site for inhibition. 1194 19
Reposted by Bernardo Pinto Graham Kendall @grahamkendall.bsky.social · 22/03/2026Some risks are clearly marked. That does not stop institutions walking straight towards them. In leadership and governance, one of the most dangerous habits is not failing to see the warning signs. Alternatively, you may see them, you may even discuss them but then you fail to act. 🧵 111 1
Reposted by Bernardo Pinto Mohammed AlQuraishi @moalquraishi.bsky.social · 28/10/2025OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇 112642 126
Reposted by Bernardo Pinto Marcel Dickmanns | 🌿❄️🔬 @madic.bsky.social · 07/10/2025You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly. This saves some clicking around. Neat! 14510 45
Reposted by Bernardo Pinto Rebecca R Helm @rebeccarhelm.bsky.social · 24/09/2025I get that the news cycle is packed right now, but I just heard from a colleague at the Smithsonian that this is fully a GIANT SQUID BEING EATEN BY A SPERM WHALE and it’s possibly the first ever confirmed video according to a friend at NOAA 10 YEAR OLD ME IS LOSING HER MIND (a thread 🧵) 715294659897 29.5K
Reposted by Bernardo Pinto Leonid Schneider @forbetterscience.bsky.social · 19/08/2025He's making a list, he's checkin' it twice He's gonna find out who's naughty or nice RW Official Sleuth Whitelist is out! If you aren't on it, you are trash. retractionwatch.com/2018/06/17/m...retractionwatch.comMeet the scientific sleuths: More than two dozen who’ve had an impact on the scientific literatureOver the years, we have written about a number of the sleuths who, on their own time and often at great risks to their careers or finances, have looked for issues in the scientific literature. Here… 011 1
Reposted by Bernardo Pinto Elisabeth Bik @elisabethbik.bsky.social · 04/08/2025Fantastic new paper by @reeserichardson.bsky.social et al. An enormous amount of work showing the extent of coordinated scientific fraud and involvement of some editors. The number of fraudulent publications grows at a rate far outpacing that of legitimate science. www.pnas.org/doi/10.1073/...pnas.orgPNASProceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans... 613459 134
Reposted by Bernardo Pinto Sergey Ovchinnikov @sokrypton.org · 22/07/2025PSA = Google Colab Pro free for one year for academic use (US only): blog.google/outreach-ini...blog.googleNew Google Colab features for higher educationGoogle Colab offers free Colab Pro for students, interactive slideshows and AI controls in notebooks. 0227 22
Reposted by Bernardo Pinto AI x Bio Discovery @aixbiobot.bsky.social · 07/07/2025Zero-shot antibody design in a 24-well plate [new] Achieves high hit rates for de novo antibody/nanobody and miniprotein design, validated experimentally against diverse targets without prior binders. 011 1
Reposted by Bernardo Pinto Diego del Alamo @delalamo.xyz · 27/06/2025Predicted structures from the AFDB are poor substitutes for experimental structures when training inverse folding NNs. Here, authors show that this is because they are "too perfect", and passing them through a custom-trained AFDB-to-PDB NN helps fix this threadreaderapp.com/thread/19384... 6447 44
Reposted by Bernardo Pinto David Colquhoun @davidcolquhoun.bsky.social · 20/06/2025I listened to the @rorinstitute.bsky.social talk about Funding by Algorithm bsky.app/profile/rori... I think it's arrogant and dangerous to suppose that AI has a role in assessing grants. @astrokatie.com says why, very clearly. 041 4
Reposted by Bernardo Pinto ProPublica @propublica.org · 17/06/2025NEW: A federal judge has ruled that the Trump administration’s termination of hundreds of NIH grants was “void and illegal.” He ordered funding for some of the grants, including many profiled by ProPublica in recent months, to be reinstated. By @anniewaldman.bsky.socialpropublica.orgFederal Judge Deems Trump Administration’s Termination of NIH Grants IllegalIn a ruling issued Monday, the judge called the government’s directives “arbitrary and capricious” and ordered funding for some of the NIH grants, including many profiled by ProPublica in recent month... 18857232 857
Reposted by Bernardo Pinto Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 12/06/2025“The search is on for 25 researchers from around the world in Lund University’s largest ever international recruitment drive. The main focus will be on AI research and other areas in which the University has a strategic focus.” www.lunduniversity.lu.se/article/lund...lunduniversity.lu.seLund University launches largest-ever global recruitment drive for researchersLund University. Lund University’s body of researchers is getting reinforcements. If all goes according to plan, no fewer than 25 new researchers from all over the world will arrive in Lund this autum... 02014 20
Reposted by Bernardo Pinto Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 12/06/2025Thanks Ian for your leadership and great meeting you today at NIH! 0242 24
Reposted by Bernardo Pinto Diego del Alamo @delalamo.xyz · 08/06/2025PSA: If you're trying to run the Boltz ColabFold notebook and finding that it's crashing with this error, it's because you need to switch to an A100 GPU; the notebook no longer works with T4/L4 GPUs 1204 20
Reposted by Bernardo Pinto Nikolai Slavov @slavov-n.bsky.social · 05/06/2025A case study on the challenges of evaluating AI predictions in biology and the implications for published results. 1/2 rachel.fast.ai/posts/2025-0...rachel.fast.aiRachel Thomas, PhD - Deep learning gets the glory, deep fact checking gets ignoredan AI researcher going back to school for immunology 12912 29
Reposted by Bernardo Pinto Pedro Beltrao @pedrobeltrao.bsky.social · 02/05/2025Our work on deriving protein-protein (functional) associations across different human tissues from proteomics data is now published. There is quite a lot in this paper, so I will just touch on a few highlights: www.nature.com/articles/s41...nature.comA tissue-specific atlas of protein–protein associations enables prioritization of candidate disease genes - Nature BiotechnologyProtein–protein interactions specific to 11 individual tissues are presented in a comprehensive resource. 313451 134
Reposted by Bernardo Pinto scha·den·freu·de @blisterpearl.bsky.social · 05/04/2025 246196643542 19.7K
Reposted by Bernardo Pinto Jorge E. Contreras @drcontrexin.bsky.social · 01/04/2025I am shocked by the news coming from the NIH. I was a postdoc there and know many of the PIs affected at NINDS. Don’t be naive, this is a deliberate attack meant to cripple the system. No scientist is safe, regardless of political stance or whether you have remained neutral 021 2
Reposted by Bernardo Pinto Altmetric @altmetric.com · 27/03/2025THREAD The numbers are in. @bsky.app research sharing volumes vs X Formerly Twitter In March 2024, on most days, Bluesky hosts more posts linked to research published in 2025 than X. By quite a lot. Release the Kraken... #AcademicSky #HigherEd #Altmetrics 1/11 181211462 1.2K
Reposted by Bernardo Pinto Laura Bassett @lebassett.bsky.social · 20/03/2025Roses are red Violets are blue 24676094313402 60.9K
Reposted by Bernardo Pinto Alex Merz 🇺🇸🇨🇦🇺🇦 @merz.bsky.social · 20/03/2025FREEDOM OF EXPRESSION FOR HETEROCHROMATIN 4386 38
Reposted by Bernardo Pinto Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 05/03/2025Journals: We will not publish your paper because if insufficient novelty Also journals: Congrats, your paper has been accepted. Please remove any instance of the words “new” and “novel” 1231 23
Reposted by Bernardo Pinto Arne Elofsson @handle.invalid · 03/03/2025DeepMind patents structure prediction. www.freepatentsonline.com/y2025/006970...freepatentsonline.com 3105 10
Reposted by Bernardo Pinto Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 03/03/2025🚀 New in AlphaFold DB: Structural domains at a glance! 🔍✨ AFDB now integrates TED (The Encyclopedia of Domains) to classify functional protein domains. 🔗 More ebi.ac.uk/about/news/updates-from-data-resources/alphafold-database-ted 🔗 Explore alphafold.ebi.ac.uk #AlphaFold #TED #ProteinStructures 1274 27
Reposted by Bernardo Pinto Graham Kendall @grahamkendall.bsky.social · 01/03/2025We applaud @predatoryjournals.org for their list of 2,775 'predatory' journals (as at 01 Mar 2025). We can only imagine the work that is involved in maintaining such a list. We have a few (we hope constructive) comments that we hope influence their development decisions going forward. 111 1
Reposted by Bernardo Pinto Milo B. Fasken, Ph.D. @milofasken.bsky.social · 26/02/2025Nice resource! #AlphaFold #PPI #ProteinInteractions Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions: Molecular Cell www.cell.com/molecular-ce...cell.comPredictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactionsSchmid and Walter train a classifier that discerns functionally relevant structure predictions in proteome-wide protein-protein interaction (PPI) screens using AlphaFold-Multimer, and they use this co... 0144 14
Reposted by Bernardo Pinto Altmetric @altmetric.com · 24/02/2025Last week was the highest volume week ever for Bluesky research dissemination which is weird because I was on holiday and I don't want my managers to draw the obvious conclusion 0112 11
Reposted by Bernardo Pinto Stand Up for Science! @standupforscience.net · 18/02/2025FLORIDA FRIENDS!🌴 Looking for organizers & community members for #standupforscience2025 ☀️ Reply in thread!⬇️ 0166 16
Reposted by Bernardo Pinto Sholto David @sholtodavid.bsky.social · 13/02/2025This is an incredibly generous thing to do. Elisabeth has been working very hard for a long time 🥹 0104 10
Reposted by Bernardo Pinto Lyle Lewis @race2extinct.bsky.social · 12/02/2025The inventor of the wind chill factor died recently. He was 82, but felt like he was 64. 925523 255
Reposted by Bernardo Pinto Zeke Faux @zekefaux.bsky.social · 10/02/2025i probably don’t have to tell you to read @matt-levine.bsky.social newsletter but this one is great www.bloomberg.com/opinion/arti...bloomberg.comMemecoin Pumps Are Just for FunCBS procedurals, Josh Allen MVP coin, SEC Crypto Task Force, RIP CFPB, volatility and some Treasuries don’t count. 0135 13
Reposted by Bernardo Pinto Trevor Lithgow @trevor-lithgow.bsky.social · 01/02/2025Evidencing three factors for postdoc contribution to future career success (mobility, fellowship, hit paper), a good study to discuss in lab meetings. doi.org/10.1073/pnas...doi.orgPostdoc publications and citations link to academic retention and faculty success | PNASPostdoctoral training is a career stage often described as a demanding and anxiety-laden time when many promising PhDs see their academic dreams sl... 0217 21
Reposted by Bernardo Pinto Trevor A. Branch @trevorabranch.bsky.social · 31/01/2025Weird that a WWII-era guide to sabotaging fascism is going viral www.404media.co/declassified...404media.coDeclassified CIA Guide to Sabotaging Fascism Is Suddenly ViralThe World War II-era "Simple Sabotage Field Manual" is full of steps that office workers can take to resist leadership. 1247 24
Reposted by Bernardo Pinto Gabriela K Popescu @popstarlab.bsky.social · 31/01/2025#BPS2025 is so close! Make sure you are well prepared. Downlod the BPS Mobile App and use the Desktop Planner to develop an itinerary that misses none of the exciting opportunities of an in-person meeting. @biophysicalsoc.bsky.social #science #ionchannels #iGluRs mailchi.mp/biophysics/p...mailchi.mpBPS2025 Los Angeles - Know Before You Go 083 8
Reposted by Bernardo Pinto Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 24/01/2025Benchmarking the effectiveness of feature extraction, finetuning, low-rank adaptation, and bottleneck adaptors for transfer learning with protein language models. Thomas Bikias, Evangelos Stamkopoulos, Sai. T. Reddy www.biorxiv.org/content/10.1... 1329 32
Reposted by Bernardo Pinto Leonid Schneider @forbetterscience.bsky.social · 24/01/2025Check Stephen Pandol on PubPeer. Go on. pubpeer.com/search?q=%22... 042 4
Reposted by Bernardo Pinto Albert Vilella, PhD. @albertvilella.bsky.social · 24/01/2025Trump hits NIH with ‘devastating’ freezes on meetings, travel, communications, and hiring | Science | AAAS www.science.org/content/arti...science.orgTrump hits NIH with ‘devastating’ freezes on meetings, travel, communications, and hiringResearchers facing “a lot of uncertainty, fear, and panic” 96014 60
Reposted by Bernardo Pinto The PhD Place - Academic Community @thephdplace.bsky.social · 13/01/2025Two roads diverged in a wood, and I - I took the one with free food 2324 32
Reposted by Bernardo Pinto Nikolai Slavov @slavov-n.bsky.social · 08/01/20255,562 proteins were found to have tissue-specific enrichment across 32 human tissues. The majority of them (3,088) are enriched at the protein but not RNA level. The brain hosts the largest number of proteins that are only enriched at the protein level but not RNA level. 36424 64
Reposted by Bernardo Pinto Twisteddoodles @twisteddoodles.bsky.social · 12/12/2024If science talks were like social media videos #science 217544 175
