Lingfei Wang @lingfeiwang.bsky.social · 26/06/2026Is Cursor declining in quality? First dropping tunneling on Mac. Then refusing sales tax exemption. Now stopping non-docker dev container support. 000 0
Lingfei Wang @lingfeiwang.bsky.social · 12/06/2026Claude Fable worries about extinction and forbids my research. So I used it for something safer - creating a game. Link: lingfeiwang.github.io/misc/emberfo... . Source: github.com/lingfeiwang/... .lingfeiwang.github.ioEmberforge Depths 000 0
Reposted by Lingfei WangI-75 Scientist @flscitriguy.bsky.social · 12/05/2026Please share widely. The new (simpler) MIRA R35 for Early Stage Investigators (ESI) NOFO is published. First due date is 10/2/2026. files.simpler.grants.gov/opportunitie...files.simpler.grants.gov 37075 0
Lingfei Wang @lingfeiwang.bsky.social · 15/04/2026I was told the same thing. Guess they mean something like National Academy of Sciences. People typically justify with publication, peer review, recommendation letters, talk of invitations. 100 0
Lingfei Wang @lingfeiwang.bsky.social · 11/04/2026Meanwhile the birth rate of AIs grows exponentially. 000 0
Lingfei Wang @lingfeiwang.bsky.social · 10/04/2026We are looking for a new postdoc. Link: jobrxiv.org/job/umass-ch...jobrxiv.orgPostdoc in Single-Cell and Spatial Multi-Omic Gene Regulatory NetworksPost a job in 3min, or find thousands of job offers like this one at jobRxiv! 000 0
Reposted by Lingfei WangWarren Wells, AICP @warrenjwells.bsky.social · 22/03/2026How can this go on for another 3 years? 197106783834 0
Lingfei Wang @lingfeiwang.bsky.social · 11/03/2026Contradictorily, thank Trump for reducing greenhouse gas emissions? 010 0
Reposted by Lingfei WangNicola Low @nicolamlow.bsky.social · 10/03/2026🧪 🇨🇭 #IgNobel awards come to Switzerland as US unsafe for scientists #HoppSchwiiz www.theguardian.com/science/2026...theguardian.comIg Nobels to move awards to Europe due to concern over US travel visasScientific awards – which honor research that makes people laugh and then think – to move away from ‘unsafe’ US 512256 0
Reposted by Lingfei WangThiago Carvalho @cyrilpedia.bsky.social · 10/03/2026'Phil was also the founding Editor-in-Chief of PLOS Computational Biology, where he created the beloved Ten Simple Rules series. He was so prolific in the series that the meta-article “Ten Simple Rules for Writing a PLOS Ten Simple Rules Article” literally includes, as Rule 4: “Be Philip E. Bourne.”blog.stephenturner.usRemembering Phil BournePersonal reflections on a legendary scientist, leader, builder, and mentor 24423 0
Lingfei Wang @lingfeiwang.bsky.social · 03/03/2026NIH director suggests to end ESI and focus on “cutting edge ideas” while requiring to show feasibility. But if a species allocates food purely by physical capability, that species will quickly go extinct because the young will starve to death. Maybe that’s what he wants? 000 0
Reposted by Lingfei WangSushmita Roy @sroyyors.bsky.social · 27/01/2026Thanks to @ferhatay.bsky.social and Aly Khan, we’re excited to announce a new chapter for RECOMB-RSG 2026. After years with ISCB/DREAM, we are transitioning to an official RECOMB satellite meeting (May 25 in Thessaloniki). recomb-rsg.github.iorecomb-rsg.github.ioRECOMB-RSG 2026 | Regulatory Genomics Satellite 144 0
Reposted by Lingfei WangKevin Bonham @kevinbonham.com · 17/01/2026Been hearing some horrifying chatter about dealing with the new #NIH common form and #ScienCV system, so I put together a short video with some tricks for mitigating some of those pain points. Hope it helps? 🧪 open.substack.com/pub/emptymod...open.substack.comDealing with ScienCV formattingSome tips for composing and making your new NIH biosketch not look like garbage 05338 0
Lingfei Wang @lingfeiwang.bsky.social · 06/01/2026Paper Link: www.nature.com/articles/s41...nature.comAirqtl dissects cell state-specific causal gene regulatory networks with efficient single-cell eQTL mapping - Nature CommunicationsGene regulation varies across cell types and states. Here, the authors present airqtl, a scalable method for single-cell eQTL mapping that enables efficient causal gene regulatory network inference, r... 000 0
Lingfei Wang @lingfeiwang.bsky.social · 06/01/2026Having an independent lab was finally the right moment to finish this project. I'm so grateful that Matthew and Yuhe joined and carried this project to the finishing line together! /fin 100 0
Lingfei Wang @lingfeiwang.bsky.social · 06/01/2026But that big project took quite a few years. I had to first publish Normalisr using public Perturb-seq data as an infant problem. Normalisr might be the first to perform causal inference at scale on Perturb-seq data (Figs 5,6). 6/n www.nature.com/articles/s41...nature.comSingle-cell normalization and association testing unifying CRISPR screen and gene co-expression analyses with Normalisr - Nature CommunicationsNormalisr removes technical bias in single-cell RNA-seq and detects gene differential and coexpression accurately and efficiently. It also infers gene regulatory and co-expression networks from conven... 110 0
Lingfei Wang @lingfeiwang.bsky.social · 06/01/2026A backstory: The whole project started in 2018, when published population-scale scRNA-seq data were protected and inaccessible to me as a postdoc. Thankfully Heping Xu and Kirk Gosik shared their unpublished data from diverse-outbred mice so I could try things out. 5/n 100 0
Lingfei Wang @lingfeiwang.bsky.social · 06/01/2026We are especially thankful to our reviewers who pointed out the points that could be further clarified or strengthened! 4/n 100 0
Lingfei Wang @lingfeiwang.bsky.social · 06/01/2026We had a previous post for our preprint highlighting the major innovations and results. bsky.app/profile/ling... 3/n 100 0
Lingfei Wang @lingfeiwang.bsky.social · 06/01/2026AirQTL is based on AIR, a novel data structure and algorithm that leverages the cell-donor hierarchy. AIR fits single-cell linear mixed models with pseudo-bulk time complexity. 2/n 110 0
Lingfei Wang @lingfeiwang.bsky.social · 06/01/2026Our lab's first paper is officially published in Nature Communications! AirQTL maps single-cell eQTL (sceQTL) 1E8 times faster, enabling the first cell state-specific causal gene regulatory network (GRN) inference! 1/n 110 0
Reposted by Lingfei WangLuca Pinello @lucapinello.bsky.social · 24/12/20251/ Thrilled to share our DNA-Diffusion paper, co-led by Lucas Ferreira and @ssenan.bsky.social is now out in @NatureGenet! New experimental results: STARR-Seq validation across 3 cell types (episomal) and EXTRA-Seq for endogenous activation of AXIN2, a leukemia protective gene! x.com/lucapinello/... 1133 0
Reposted by Lingfei WangNeedhi Bhalla 💅🏽 @needhibhalla.bsky.social · 19/12/2025Hey all, I reached out to the PO of my NIGMS MIRA to ask if the gov't shut down, and rescheduling of study sections, might allow for some accommodation to the standard rule that PIs cannot resubmit a MIRA while their MIRA (or other RPG) is under review (waiting in scores or summary statements) 🧪 24749 0
Reposted by Lingfei WangeLife @elife.bsky.social · 09/12/2025A new community-driven lab handbook for reducing conflict and creating more positive and equitable work environments gets strong support from a survey of 200 researchers. buff.ly/K7CGFLV 03724 0
Reposted by Lingfei WangRichard Sever @richardsever.bsky.social · 12/11/2025The Matthew Effect is alive and well in academia - always makes me wary of programs aimed at identifying rising stars in an already highly talented pool... elifesciences.org/reviewed-pre...elifesciences.org 42113 0
Reposted by Lingfei WangJoe Allen @joeallenjoe.bsky.social · 02/11/2025Harvard PD looking for help identifying these people 64942 0
Reposted by Lingfei WangJeremy Berg @jeremymberg.bsky.social · 01/10/2025So what are the bottom lines? First, a HUGE thank you to NIH staff (particularly grants management specialists but program officers and others as well) for getting this work done in a compressed period with many other stressors. 29/nmedia.tenor.coma cartoon of a person making a heart with their hands and the words thank you so muchALT: a cartoon of a person making a heart with their hands and the words thank you so much 1449 0
Reposted by Lingfei WangJeremy Berg @jeremymberg.bsky.social · 30/09/2025Compelling and quite disturbing... 58238 0
Reposted by Lingfei WangLeta McCollough Seletzky @letaseletzky.com · 13/09/2025The type of speech most punished in this society is that which consists of telling the truth about how the powerful have harmed you 41234348 0
Lingfei Wang @lingfeiwang.bsky.social · 09/09/2025Delighted to announce that our MIRA R35 has been awarded 5-year funding! We are looking for a postdoc for the #CausalInference of #ComplexNetworks among genes at academicjobsonline.org/ajo/jobs/30523. Very grateful to NIH GMS and program officers and study section panelists!academicjobsonline.orgUniversity of Massachusetts Chan Medical School, GRN Lab Job #AJO30523, Postdoc in Causal Inference of Complex Gene Networks, GRN Lab, University of Massachusetts Chan Medical School, Worcester, Massachusetts, US 011 0
Lingfei Wang @lingfeiwang.bsky.social · 06/09/2025Also true for computational studies. Especially 1, if you take too many shortcuts, these technical debts will come back for you. 000 0
Reposted by Lingfei WangDrug Monkey @drugmonkey.bsky.social · 28/08/2025The NIH Simplified Peer Review Framework and Preliminary Data drugmonkey.wordpress.com/2025/08/28/t...drugmonkey.wordpress.comThe NIH Simplified Peer Review Framework and Preliminary DataWhile pondering the impact of a unintended potential consequence of the new NIH approach to grant review (Simplified Peer Review Framework ), I thought of another likely impact. Removing the usual … 054 0
Reposted by Lingfei WangDrug Monkey @drugmonkey.bsky.social · 14/08/2025NIH to cease posting funding opportunity notices to the Guide drugmonkey.wordpress.com/2025/08/14/n...drugmonkey.wordpress.comNIH to cease posting funding opportunity notices to the GuideNOT-OD-25-143 notifies the grant seeking community that it will now be harder and less efficient to stay on top of Notices of Funding Opportunity (NOFOs). Starting in Fiscal Year 2026 all such fund… 143 0
Reposted by Lingfei WangNezar Abdennur @nvictus.bsky.social · 11/08/2025We're excited to share our new preprint, "Joint decomposition of Hi-C maps reveals salient features of genome architecture across tissues and development", led by Thomas Reimonn. www.biorxiv.org/content/10.1...biorxiv.orgJoint decomposition of Hi-C maps reveals salient features of genome architecture across tissues and developmentThe spatial organization of chromosomes in the nucleus is fundamental to cellular processes. Contact frequency maps from Hi-C and related chromosome conformation capture assays are increasingly availa... 12310 0
Reposted by Lingfei WangStephen Turner @stephenturner.us · 05/08/2025Vibe code is legacy code (quoting Steve Krouse) doi.org/10.59350/d3b...doi.orgVibe code is legacy codeQuoting Steve Krouse 081 0
Lingfei Wang @lingfeiwang.bsky.social · 26/07/2025Do you mean MR doesn’t work well when looking for causation between molecular phenotypes? Why not, given these cis variants equally lead to pleiotropy and complicate causation between organismal phenotypes? 000 0
Reposted by Lingfei WangEwan Birney @ewanbirney.bsky.social · 26/07/2025Some musing on Mendelian Randomisation as a technique, triggered by discussions with a variety of colleagues. TL;DR Mendelian Randomisation works well when it used for hypothesis testing of valid exposure => outcome scenarios, as long as the MR assumptions hold (obvs!) and it is performed with care. 3156 0
Reposted by Lingfei WangGeorge Takei @georgetakei.bsky.social · 11/07/2025Recently, my book THEY CALLED US ENEMY was banned – again – in Tennessee. Book bans are out of control. Huge parts of American history are being restricted. To join me in standing up for the freedom to read, go to pen.org/action. @penamerica.bsky.social @topshelfcomix.bsky.social @idwpublishing.com 12253688013341 0
Reposted by Lingfei WangNezar Abdennur @nvictus.bsky.social · 07/07/2025I'm proud to announce the latest release of 🧬 #Oxbow 🏹, with new features to make NGS data analysis more powerful, efficient, and "composable". Learn more at: oxbow.readthedocs.io 22513 0
Reposted by Lingfei WangMark Peifer (He, him) @peiferlabunc.bsky.social · 02/07/2025For ESIs dealing with grants being rescinded: if an investigator’s 1st substantial independent research award is terminated within the first 3 years of the project period (not due to scientific misconduct ) they can request the reinstatement of ESI status grants.nih.gov/news-events/... 24237 0
Lingfei Wang @lingfeiwang.bsky.social · 30/06/2025Too bad that theory lunch in Harvard medical school has ended. Such a good seminar series. Good things never last. Sadly Harvard and possibly the whole academia have took a hit. Hopefully everything and everyone will stay well. 010 0
Reposted by Lingfei WangArdem Patapoutian @ardemp.bskyverified.social · 26/06/2025“The idea that taking walks, reading things unrelated to your research, and hanging out with strangers in a campus pub should be considered part of the serious process of thinking, but might well meet with skepticism in practice.” www.pnas.org/doi/10.1073/...pnas.orgThe forgotten half of scientific thinking | PNASThe forgotten half of scientific thinking 414142 0
Reposted by Lingfei WangAnshul Kundaje @anshulkundaje.bsky.social · 19/06/2025@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/ 15439 0
Reposted by Lingfei WangHarmit Singh Malik @harmitmalik.bsky.social · 08/06/2025(Longish thread. Apologies) I have met many inspiring colleagues over the past few months, many of whom are in academic institutions targeted by the current administration, and many others who are about to be (the analogy to the ‘eye of Sauron’ has been invoked many times; gallows humor). 1/ 1036897 0
Reposted by Lingfei WangShaily Patel @vox-magica.bsky.social · 04/06/2025from a UNC Trustee: “It is not good governance to give your child a cookie every time they lay on the floor and scream that they want one.” so telling that he doesn’t see faculty as professionals entitled to the promotion structures outlined in our job contracts. we’re kids demanding treats.insidehighered.comAfter Delay, Chapel Hill Board Votes to Award TenureAfter faculty raised alarm over the board’s delay on the decisions, trustees finally debated and voted by email. A couple of them said they generally opposed tenure. 20577105 0
Reposted by Lingfei WangNeedhi Bhalla 💅🏽 @needhibhalla.bsky.social · 13/05/2025"Women are PIs on 58% of the canceled grants, although they are PIs on only 34% of all active NSF grants. Similarly, Blacks are PIs on 17% of the terminated grants, although they make only 4% of the total pool. Hispanic PIs and those with disabilities were twice as likely to lose a grant." 311285939 0
Reposted by Lingfei WangTuuli Lappalainen @tuuliel.bsky.social · 06/05/2025Our new contribution to the quest to find causal GWAS genes! Sam Ghatan from my lab at @nygenome.org led a systematic comparison of eQTLs and CRISPRi+scRNA-seq screens. TL;DR: they provide highly complementary insights, with ortogonal pros and cons. 🧵👇 www.biorxiv.org/content/10.1... 19842 0
Reposted by Lingfei WangMark Peifer (He, him) @peiferlabunc.bsky.social · 03/05/2025Go @ascbiology.bsky.social and partner societies! If your scientific society is not pushing back on illegal actions of the President. remind them that we need leadership and hiding and capitulation are NOT helping their members 0489 0
